Secrets
by sgafan360
Summary: Everyone has Secrets John Sheppard happens to have the greatest of them all. Completed finally. SHEYLA. Sorry for horrible updating.
1. Chapter 1

Spoilers for Quarantine, Ark of truth, Last Man, and possibly Continuum, all of SG-1 and everything in Atlantis up to BAMSR it should basically be just a reference or two for most of them and obviously most of the episodes are not going to be referenced. Everything is accepted as seen on screen until after BAMSR. I'll also be referencing other eps throughout the seasons but events in them may be changed based on how it differs.

Pairings: John/Teyla (main)

There is also a crossover of some SG-1 character during later chapters.

Chapter 1

She regretted having to tell him what to do but someone needed to and as his commanding officer it was her responsibility. She remembered how she felt when her team had been ordered to replace Daniel although he had died and Teyla was only pregnant but still you never liked to replace a member of your team. "Are you sure you don't want someone else to accompany your team on this mission Colonel," Colonel Carter asked.

"Yes we will be fine without Teyla for time being," he responded.

"For this mission you may proceed with a three man team however you will have to choose a temporary replacement until you place Teyla back on active duty."

"Understood Colonel," Colonel Sheppard said before turning around and heading through the wormhole. On the other side the team walked in silence for a few minutes before Ronon decided to break it.

"Who are you going to choose to replace Teyla?"

"Haven't really put much thought into it don't really want to either," he said attempting to kill the conversation however Rodney had other ideas.

'You're the one who took her off of active duty."

"Yes Rodney I can't have her going off world while she's pregnant."

"I suppose but still."

"You're not actually suggesting that we have pregnant women out hunting the wraith?"

"Wait I'm picking up an energy signature," Rodney said quickly.

"Do you ever not pick up an energy signature?"

"Yes but this one is very large."

"Let's go check it out," he ordered glad for distraction albeit a boring one.

They walked through the forest for another half an hour and entered a clearing where they saw a massive structure, "I think we found your power signature."

"Actually for a building that size the signature is pretty small."

"How small?"

"A single generator," Rodney said clearly disappointed.

"Well we better check it out anyway." Sheppard said once again heading to the structure.

Ronon grunted and followed them towards the Ancient facility. Upon entering the facility the team split up with Rodney going after the energy source Ronon wondering aimlessly and John heading to the control room. When Sheppard entered the control room it lit up as usual however he noticed that there was a large life signs like detector or one of the walls, "Rodney you might want to get up here."

"Sheppard what did you just do I'm reading a 200% increase in power."

"I just turned everything on you might want to get up here though Rodney."

"Yes, yes I'll be right there." He said before heading in the direction Sheppard had gone.

Rodney arrived hooked up his Tablet and began taking some readings. After a few minutes John sat down resting on a nearby wall and fell asleep while Rodney continued to work. A few minutes later Rodney woke him, "Hey Sheppard you might want to see this."Sheppard, unhappy at being roused from his sleep simply grumbled as he got up.

"I think I know what this place does," Rodney said cheerily.

"And what does it do Rodney?"

"It's the Ancients long range sensors largest sensor array."

"Don't we have those on Atlantis?"

"Well yes and no yes in that we do and no in that these sensors are much more powerful they contain data for this entire galaxy and surrounding area," Rodney said excitedly tapping on his Tablet as he moved around the room.

"And what does that mean Rodney?"

"We will know where every single vessel capable of Space flight is in this galaxy."

"So?"

Now starting to get annoyed Rodney tried one last time to get him to understand, "Well if the ancients left any ships than we can retrieve those we can see where the wraith are going to cull however I don't know what these signatures are both different colors and yet only one of each in the galaxy."

"New types of ships?"

"It's a possibility well have to check it out or it could be previously undiscovered ancient ships."

"Ronon were going back to the gate McKay found something important that he wants to bring back to Carter."

"Meet you back at the gate," he said quickly before ending the communications link.

On the way back to the gate Rodney tried to talk with John however he was unresponsive and what few answers he gave were vague and nondescript after several minutes. Sheppard had to tell Rodney to be quiet after which Rodney did finally. They made their way through the gate without anything eventful happening. Rodney held a briefing a few hours after returning with most of the senior staff present.

"Of what I've gathered this is the ancient's largest sensor array in the galaxy its range easily encompasses this galaxy and a good deal of the nearby space. "

"How small can it detect down to?" Colonel Carter inquired

"I think I saw jumpers and darts however there were some unidentified signals"

"How many?"

"Two or three one is actually on a planet and I checked the sensor logs a bit and I think that it hasn't moved since the ancients first left this galaxy."

"All right let's move on it you leave tomorrow take SGA-2 as backup and Colonel Sheppard a word."

They departed except Colonel Sheppard who remained to talk to Carter, "yes Colonel"

"Are you considering filling Teyla's position on the team?"

"Not yet I don't think I will be able to find anyone who can replace her," he meant it in more ways then Carter thought.

"I understand however you will have to add a fourth member after this mission."

End Chapter 1


	2. Chapter 2

Chapter 2

"How was the team's last mission Ronon?" Teyla asked sitting in the commissary eating dinner with Ronon.

"It went well I guess Rodney found something that excited him so we came back here" he said dryly

"You did not seem to enjoy it"

"Nothing to do on these missions" he said sounding disappointed

"How is John?"

"He's not himself and I really don't think that he likes the idea of replacing you"

"He is the one who took me off duty"

"Well did you really think he would let you continue?"

"No" she admitted

"So have you decided what you're going to name him?"

"I have not"

"You don't want Ronon" he asked half joking

"I do not" she said smiling

"Well I hope we find your people before"

"As do I" she said cutting him off

"Do you think Colonel Sheppard will allow me to rejoin the team after the child is born?"

"I don't see why he wouldn't but I don't know they might do things differently" he said indicating the Earth natives

"Yes it would be disappointing if I were no longer allowed to join the fight against the wraith"

"Ask Sheppard" he told her

"We have not spoken much since I told him"

"Ronon, Teyla" Sheppard said joining the conversation although he didn't sit down or have any food.

"Colonel Sheppard" Teyla responded looking at him

"Sheppard what's up?" Ronon asked while continuing to eat

"Were going after a ship only one of its kind in the galaxy" he informed the pair

"What kind?" he asked despite not really caring.

"No idea that's why we're going" he said semi enthusiastically

"When are we leaving?"

"Tomorrow morning just thought I'd let you know" he said before turning around and leaving the mess hall.

"Go ask him" he said more forcefully than before.

"There are several months before it will become an issue"

"But if you ask him now than he will have several months to think about it"

"And if he says no"

"He won't" he stated

"I do not share your optimism but I will ask him" she said getting up and leaving following Sheppard. After a few minutes she managed to catch up to him. "Colonel Sheppard"

He spun around "yeah"

"I wish to speak with you" she said catching up to where he stood

"I'm not letting you on this mission" he said and started walking again

"It is not about that John" she said walking beside him towards wherever he was going

"What is it about then?"

"Ronon and I were wondering if I would be allowed to rejoin the team after the child is born"

"I don't know Teyla I will have to think about it but are you sure you're going to even want to rejoin the team I mean you will have a baby to look after"

"I do not wish to stop fighting the wraith simply because I have a child"

"You might change your mind when you see and hold him for the first time"

"That is possible but if I do not"

"Then I will take it under consideration"

"That is all I ask thank you john" she said content with his answer.

"No problem" he responded instinctively before turning a corner leaving her alone to consider what he said. She returned to her quarters finding that she became tired much more easily now than she had before.

"All right Major Lorne you and your team will stay with the jumper if we can't find anywhere near the ship to land"

"Let's move out he said as he brought the jumper through the gate"

"Rodney you getting anything"

"Nope nothing could be cloaked though"

"But still picked up on that sensor"

"Apparently"

"Any ideas of where to start"

"Yeah how about over those mountains it's possible they might be blocking some signals"

"Mountains it is than" he said flying over towards them. After climbing over them they saw a large caldera with a small ship in the center"

"That's the ship?"

"Apparently"

"Looks pretty small to me McKay" Ronon critiqued

"Yes well look how small these jumpers are and how advanced are they"

"Yes but these go through the gate that ship is not fitting into a gate" he observed

"Fine than let's leave the advanced ship that is emitting absolutely nothing in the middle of a caldera so that the villagers armed with arrows can come and use it" Sarcasm evident in his voice

"I never said we wouldn't check it out it just doesn't look that good and what do you know no bays on the ship" Sheppard reassured him

"Well it's probably not a carrier might just be a scout or a personal ship who knows"

"You think the Ancients had personal spaceships"

"Maybe I don't know but that's not the point"

"Relax Rodney"

"Lorne you and your team stay with the jumper well escort Rodney to the ship"

They once again walk in silence leading Rodney to ponder why they no longer talk to each other like they once did. _Hmm why are things nicer now I mean it used to be torture to have to walk through these jungles while listening to Sheppard go on and on about something which has absolutely no scientific merit whatsoever. Actually why isn't Sheppard talking at all usually it takes someone to sense someone about to shoot me before he shuts up. Actually he hasn't been all that talkative lately I mean he is always giving me these looks when I say something to him and he just sort of disappears when we get back to Atlantis hmm I wonder what he's doing therapy maybe? No Sheppard would never go to therapy could he be seeing someone? Who? No Sheppard wouldn't be seeing anyone on base we would have heard about the pools closing and who won the bets. Dam forgot to join the bet that Teyla asks for him in the delivery room. Can I ask him what he would say is that against the rules I mean we know Ronon tried to get those two scientists that annoy me more than the rest together but he got blacklisted for that didn't he? Ah here's the ship. _

"All right now that were here you two can go off and play I've got important work to do" he said approaching what appeared to be an airlock he waved his hand in front of the sensor but nothing happened.

"What's the matter Rodney having a little problem with your important work of opening the door?" Sheppard quipped

"Yes yes very funny now get over here and see if you can open it" he said putting down his pack in order to get some of the cables.

Sheppard approached the door and swiped his hand over the sensor the door instantly responded opening up "See Rodney it isn't that hard"

"Yes yes fine now can we please go inside?"

Ronon followed them inside "So what is this place"

"I have no idea whoever built it didn't put up a sign" Rodney replied staring at his tablet before heading off somewhere

"Rodney don't you think it might be wise to wait until after we secure the ship to go off on your own" Sheppard called after him.

"There's nothing here I checked the life signs detector" he said coming back into the hallway.

"How big is it?"

"I'll let you know when I get to the bridge" he said going back around the corner.

They make their way separately through the ship Sheppard comes across what he thinks is the auxiliary control room he radios Rodney asking him if he has found the bridge yet.

"No but I found the main engine room"

"What powers the ship ZPMs?"

"No idea

"You have no idea"

"For the first time yes I have absolutely no idea what is powering this ship"

"So how do you know it's the engine room?"

"That's what the sign says"

"I thought you said they didn't put up signs"

"Apparently they do, anyway"

"Yeah well maybe the ship was stripped for parts"

"Possible"

"Sheppard did you" his statement got cut off and replaced with nothingness

"Rodney Rodney do you copy, Ronon you still there dammit this is why we wait until after we clear the ship to go wondering around" he said slamming his fists onto a nearby console which lit up immediately

"Navigational computer online please input destination"

He stared at the screen with a blank expression. "Would you like to return to Atlantis or Earth?" it said in a synthesized computer voice.

"Atlantis" he responded slightly confused and feeling uneasy.

"Confirmed, unauthorized personnel had been detected and they have now been removed primary systems are now active"

"Removed?"

"They were returned through the Stargate to Atlantis unharmed along with 4 other personnel located on the planet"

"And me"

"You are now recognized as temporary Commander of this ship, entering Hyperspace eta to Atlantis 5 minutes and as such will have limited control over the ships systems"

"Wait 5 minutes I think you have the wrong address Atlantis is across the galaxy"

"Correct Atlantis is on the other side of this galaxy of which this ship is capable of crossing in 8 minutes"

"This ship can cross the galaxy in 8 minutes?" he asked skeptically

"Correct"

"What are you?"

"An AI you would call me I control the ship in the event that my creator is not available"

"What is your creator called?"

"All files related to the creator are classified with level 1 clearance required please enter your authorization code now"

"I don't have clearance how do I get it?" he asked annoyed that the 10,000 year old computer was requesting Authorization codes from him.

"Only the creator and the current High Councilor have level 1 clearance"

"There is no High Councilor anymore"

"Correct the last High Councilor was Moros"

Sheppard sat back in the chair thinking about what to ask next

"What powers this ship?"

"I'm sorry that information is classified"

"Who built you and this ship?"

"I'm sorry that information is classified"

"Is this ship armed?"

"Yes"

"With what"

"I'm sorry that information is classified"

"Why was I not transported back to Atlantis?"

"You are not an unauthorized person"

"Can you allow them back on board this ship?"

"Confirmed doctor Rodney McKay is now allowed on this ship as are Ronon Dex and Major Lorne's team"

"How do you know their names?"

"I am in your mind"

"You are"

"Yes exiting hyperspace"

"Detecting a hyperspace window"

"What? The Daedalus isn't due back for another two weeks and the Apollo left last week" Colonel Carter asked

"It's an unidentified ship"

"Where's Sheppard when you need him, Major Lorne head to the chair room"

"Atlantis this is Sheppard" they heard over the Radio

"Colonel Sheppard is that you"

"Yes Colonel Carter tell Rodney he is going to love this ship"

"Really why Sheppard" Rodney inquired

"Well it can cross the galaxy in 8 minutes and its run by an AI"

"Permission granted Rodney"

"I didn't even ask you anything yet"

"I want to see that ship as much as you Rodney"

"Major Lorne report to the jumper bay immediately"

"Yes sir" he grumbled shuttling McKay to and from his newest toy wasn't what he had planned for when he had found himself back on Atlantis with hopefully the rest of the day off.

"Colonel Sheppard please leave the ship in orbit around the planet I don't want to risk having it land on Atlantis yet"

"Understood however I'm going to need a list of everyone that's coming up I need to clear them the ship doesn't like visitors"

"I'll have Rodney send you one as soon as he's ready.

"Understood Colonel Sheppard out" he said cutting the communications link.

"So what do I call you and the ship?"

"We carry the same name"

"And what name is that"

"We are called the Ancient"

"That's it the Ancient"

"Yes why"

"Do you have any kind of image or something?"

"Yes"

"Can I see it?"

"Activating imaging systems" he said as he appeared as a miniature version of an old man and switching his voice from the synthesized computer voice to a more natural one.

"I guess I can see why they call you the ancient"

"Actually I am named for my creator who they call the Ancient"

"Wait the Ancients called someone else the Ancient"

"Correct"

"Where is your creator?"

"I am sorry the information you have requested is classified please enter your authorization code."

"Okay please allow all these personnel access to the ship"

"They are now allowed onto the ship"

"Thank you"

Authors Note: that's chapter two once again I would appreciate any and all reviews.


	3. Chapter 3

Chapter 3

Author's Note- Sorry it took so long to post this I can't give you an ETA on when the next chapter will be posted however I do intend to continue writing the story I'm currently on chapter 10 I just hate editing it.

Sheppard stood next to the airlock waiting for it to open with the first batch of scientists. After a few minutes he heard the airlock hiss as the pressure equalized. When the door swung open Sheppard greeted the scientists and they gathered around the large entrance chamber.

"Okay Sheppard what happened last time?" Rodney asked as he stepped out of the airlock.

"The ship deemed you a security threat and removed you," he promptly answered Rodney.

"Is there a reason that it didn't send you back?" Rodney asked pointing to a corner in the room .

"Probably but it won't tell me," He said as the scientists began unpacking their gear.

"How did it send us back?"

"Teleporters I guess I don't really know."

"But the shield," Rodney started before being cut off by Sheppard.

"I think that this ship has at least some connection to Atlantis so maybe it sent some sort of code, but aren't you here to figure all that stuff out."

"Yes but I'd just like to know how it sent us and the jumper back to Atlantis and knew right where we parked," he said still pressing Sheppard for more information.

"Well it deemed you a threat and teleported you off that's about all I know."

"And I trust it won't be doing that again?" Rodney asked still nervous about being on a ship that had moved across the galaxy at unheard of speeds using unknown technology and with unknown motives.

"Nope were all on the list now," Sheppard said heading over to one of the scientists who was opening one of the airlock controls and attaching cables to it.

"Why weren't you removed with us?" Rodney said attracting Sheppard's' attention again.

"I don't know and he won't tell me," Sheppard said indicating the ships walls.

"Who's he?" Rodney asked confused

"The AI," Sheppard replied as he began meandering over towards the door looking at what each scientist was doing as he passed them. Most were still unpacking a few were standing around talking to each other.

"It's a guy?"

"Yes Rodney a very old guy actually, why what were you expecting it to be?" Sheppard said a slight hint of smugness in his voice.

Rodney ignored Sheppard's question, "What makes you think that this ship has a connection to Atlantis?"

"Just a feeling the AI mentioned that the ancients called him ancient so they had at least some contact together."

Satisfied that Sheppard had told him everything he knew, Rodney turned to his scientists, "Okay well then let's get to work."

"I'll be in the command center," Sheppard called leaving Rodney to supervise his scientists.

Rodney turned to his scientists and began issuing orders," You two go into the engine room and figure out what powers this ship, you three head to the weapon control room and figure out what kind weapons this ship has," he said pointing to the scientists.

"And you sir?" one of his new scientists asked, while the others just looked at her like she was crazy a few of them fighting to stifle their laughs.

"I will be doing everything that the five of you aren't, now let's go," Rodney replied dismissively.

His scientists shuffled out of the room following his orders. Rodney headed to the command center, before entering though he heard Sheppard talking, Rodney assumed would be the AI since he hadn't ordered any of his scientists into this section he decided that listening to what Sheppard was talking about might be interesting.

"So what are the science teams going to do?" he heard an unknown voice say from within in the room as he leaned against the wall.

"Just poke around the ship a bit, they won't do any damage, they're just trying to figure out what makes it go and what kind of weapons you have," Sheppard reassured the other voice which Rodney assumed was the AI.

"They will be unsuccessful unless they have clearance," he heard the first voice confidently declare from within.

"Yes well no one left alive has clearance," Sheppard said dryly.

"That is incorrect there are several still alive with clearance," Rodney was stunned by the AI's statement and stood against the wall with his mouth open.

"Ok non ascended beings," Rodney hastily closed his mouth realizing that Sheppard was right obviously some of the ancients who ascended would have had clearance.

"That decreases the number down to 1," Rodney was once again shocked there was someone still alive, but who?

"Wait there is someone left in human form that has clearance?" Sheppard asked shocked although a little less so than Rodney.

"That is correct," the AI said happily.

At hearing that Rodney was unable to contain himself anymore, "Who and where they are?" he demanded from the AI as he walked through the doorway. However as soon he asked the question however the AI disappeared.

Sheppard turned around to face Rodney looking very angry, "Great job Rodney you scared him away and have you been spying on me."

"No...I was...I...was just," he sputtered.

"Yeah right just do whatever you have to do and leave, I don't think this ship likes you."

"I have a lot of work to do I won't be leaving anytime soon," Rodney informed him.

"Ok Rodney just hurry up." Sheppard said moving around the room looking for somewhere to sit down.

_Several Hours later_

"THIS DOESN'T MAKE ANY SENSE," Rodney screamed at the console.

"Calm down Rodney," Sheppard said half heartedly knowing it was a wasted effort.

"But none of this stuff works it just doesn't make sense it worked for you perfectly fine a few hours earlier," Rodney said slumping to the ground next to the console that he had been working on. Sheppard stood up from where he had been sitting for the past few hours and crossed the room to where Rodney had been working.

"Maybe it's because I have the natural ATA gene and I didn't scare away the thing that runs the whole ship," He said tapping a few buttons on the dark keyboard.

"Doctor whatever her name is has it to but it doesn't work for her."

"Rodney you need to relax and calm down," He turned to the pedestal that the AI had previously inhabited. Turning around and looking upwards at the ceiling, "AI can you please tell me why this ship only responded to me?"

"Would you give up the AI hasn't been on in hours," Rodney said annoyed at Sheppard's latest attempt to turn on the AI.

"Well maybe if you hadn't scared him."

Sheppard faced Rodney again, "Well that information was very important, besides how was I supposed to know that the AI scared easily."

"I'm sure we'll eventually figure it out."

"Yes but I don't have time to wait," Rodney said impatiently as he got up off of the floor.

"Relax Rodney the ship isn't going anywhere," Sheppard said attempting to reassure the scientist.

"Ok let's try some minor systems again," Rodney said willing to try again despite the slim chances of it working.

"Which one?" Sheppard asked walking around the room randomly pressing buttons on the consoles to no affect.

"Internal sensors," Rodney said moving over to a nearby console and tapping a few keys in a vain attempt to turn it on. Sheppard watched Rodney as he once again tried to turn on a system however it still didn't work.

"OH COME ON," he screamed at the machine. After a few minutes he stopped screaming at the machine and calmed down. "Ok what are we going to do?" Rodney asked.

"About?" Sheppard replied.

"Well I haven't noticed anywhere to sleep and I don't think even I am going to be able to solve this in a day."

"You don't say, besides we could always land on Atlantis."

"What a brilliant plan let's put a ship run by an AI which managed to teleport us back through the shield that guards the gate. We have absolutely no idea what the AI plans to do for all we know it's just waiting to destroy Atlantis. And that's ignoring the fact that we can't even move the ship."

"Fine I'll have Lorne shuttle you back and forth on the jumper," Sheppard offered.

"And you?"

"I'm staying here hopefully the AI will turn back on and I can always sleep on the floor."

"I'm not doing that I've got back problems," Rodney complained.

"Ok is everyone on the ship?" Major Lorne asked.

"Yes take us back to Atlantis," Rodney managed to reply despite being engrossed in reviewing the data on his tablet.

"So why isn't Colonel Sheppard coming back."

"He wanted to stay on the ship, I have no idea why," he said dismissively turning his full attention to his tablet.

As Lorne began his descent back he reflected on the past couple of weeks and his upcoming debriefing with Carter. _Well this wasn't as bad as I thought it would be the scientists are all being quiet even Rodney isn't complaining, I guess he's got some good data on there. What did happen to Colonel Sheppard on that ship, I would have never thought that he would have wanted to stay on the ship more than Rodney. I'll probably find out at the briefing nothing to worry about I'm sure. Well hopefully I can get some sleep when we get back, yeah like that's going to happen I haven't gotten any real sleep all month. _

When he arrived he already saw his entire team around the table. "Thank you Major Lorne for taking the time to shuttle the scientists back and forth," Colonel Carter started seeing that he didn't appear to be very happy to be here.

"Do we have any idea of what that ship is?" he asked her taking a seat. He looked down at the table not really interested in the answer.

"Weren't you there sir," One of his soldiers asked.

"No, I stayed in the jumper."

"None the scientists were able to turn up anything, not even the most basic systems respond to anyone," Carter responded.

"Is there a reason Sheppard stayed on the ship?" Lorne asked Carter.

"He was hoping that the AI would come back online and talk to him."

"Do we know why the AI went offline in the first place?"

"Sheppard thinks that Rodney may have scared the AI."

"Really an AI got spooked on its own ship," he said humorously raising his head and looking at Colonel Carter.

"I share your doubt Major but so far it hasn't shown any hostile intentions."

"Where should we put the ship?"

"Well we can't put it on Atlantis, how about the mainland?"

"Sounds good to me, although I'm sure some of the scientists will still complain."

"Major can you scout out a landing site?"

"Yes Colonel," he grumbled.

"Is something wrong Major?" Colonel Carter asked concerned about his recent behavior.

"Just a little tired I haven't been sleeping well recently."

"Your scheduled for a mission tomorrow will you be good for it major?"

"Yes although I would appreciate some time off after that."

"Well Major Lorne I'll assign someone else to fly the recon mission and your team is being taken off of missions for a few days after you get back tomorrow," she said.

"Thank you Colonel."

_Earlier just after the scientists left on the ship_

Colonel Sheppard saw the last of the scientists through the airlock. _We are really going to need a better way of getting on and off this ship it can't be a good idea to have the scientists going back and forth on space walks every time they want to get on or off the ship. _

"Hello again Colonel Sheppard," the AI said.

"Hello, why did you turn off before?"

"I did not wish to the others to gain access to the ships systems, or answer Doctor McKay's questions."

"Then why did you not turn off when the first entered the ship."

"I did not notice them."

"What were you doing that had you so busy?"

"This ship has been dormant for thousands of years I needed to get it operational and absorb all the data I could."

"Where were you getting data from?"

"Atlantis among other sources."

"And I'm guessing me."

"No I am unable to enter into your memories my creator thought those much too private to allow me access to."

"Well what did you learn about us?"

"Your people are a violent one although I should not judge you."

"Yes well it is difficult to make peace with aliens who feed on you."

"No amongst yourselves you have fought many wars."

"Well we might not be the best but we certainly aren't as bad as the wraith, and why shouldn't you be one to judge."

"My creator did many horrible things and I was built with some very powerful weapons which I have used far too frequently for mine or anyone else's taste," he said sadly remorse evident on both his image and voice.

"So are you going to fight the wraith?" Sheppard asked hopefully.

"No."

"Why you said you have very powerful weapons."

"So many have died and I should not act on my own without the consent of the people or my creator."

"Then what are you going to do?" Sheppard said disappointed that he wouldn't get to see the ship in action against the wraith.

"Nothing I must wait until my creator returns, even if the people were to approve of my actions I would not act without my creator nearby."

"Well why don't you find him?"

"I cannot he is beyond my reach," Sadness creeping into his voice.

"What does that mean?"

"I am sorry that information is classified."

"Ok now what was I asking you before McKay rudely interrupted me."

"You wanted to know where was the non ascended being that has clearance, the answer is that while it is in this universe the being is within the reach of only one."

"And I'm guessing the identity of the one is classified?"

"Correct even I do not know where or who that person is although I would recognize her."

"It's a her is it?" Sheppard jokingly asked.

"Correct."

"Is there anywhere I can sleep on the ship?" Sheppard asked.

"Yes there is one bedroom here, "the AI said as a map with a flashing beacon appeared.

"Thanks if it's ok I'm going to go to sleep now."

"Do you wish for breakfast when you wake up?"

"You can do that?" He asked, totally and completely shocked, how could a 10,000 year old ship be offering him breakfast?

"Yes this ship has many different functions ranging from food to weapons to hyperspace windows."

"Well breakfast sounds nice for now." He said adding the last part with a slight smile.

"I will have one sent to you."

He thanked the AI and headed to his room where he laid down on the bed and quickly fell asleep thinking about how nice this AI was and if he should actually consider staying on the ship for an extended period of time.

_Several Weeks later_

As Sheppard sat in the chair with the few remaining scientists around him he considered his options. His first choice was to land the ship on Atlantis and put in to have his quarters reassigned since he was the only one whom the ship seemed to react to and they would learn more about the ship through his continued interaction with it. On the other hand he could request to transfer to the ship permanently there was a great deal of research to be done and he was actually enjoying this ship it had some amenities that were quite nice like the butler like AI, the ability to gloat over Rodney's incapability at controlling anything in the ship was also a huge bonus. He was quite glad when the AI had allowed Sheppard to control the ship while other people were onboard it annoyed Rodney to no end.

"_So what are you going to do?" he heard in his head the first time the AI had talked to him in his mind it scared him, now he was quite used to it although he only used it when others were on the ship and he didn't want them to hear what he was saying. He was still unsure if the AI could see into his memory despite the AI's assurances that it could not which made him more than a little uneasy. He finally thought "I have not decided."_

"_Well you do not have much time."_

_Changing the subject he went onto his daily work, "So what room am I heading to today." _

"_What would be the point if I told you what was in the rooms?" the AI teased._

"_Good point old man," he liked his nickname for the AI more than his proper name Ancient sounded so impersonal and well weird who names a ship ancient anyway. _

"_I have told you my name is ancient."_

"_And I'm calling you old man,"_ he said before getting up from the chair and heading down a hallway.

When he arrived he entered the room and began his now daily routine of flipping on all the switches and testing out what the consoles did. He knew that he was in no danger because the AI would prevent him from destroying anything that was really dangerous. He was there for half an hour, making very little progress, before Rodney came in to tell him that the final scientists were disembarking.

"Are you sure you won't come back to Atlantis?" Rodney asked.

"Yes Rodney I'm staying for a little longer, I'll be back for the briefing it's in a couple hours right?" he said without turning around and continuing to navigate the screens that were in front of him.

"Yeah Sheppard and we have a mission the day after that are you going to be ready for that?"

"Yes Rodney now can I get back to my work," he said now starting to get annoyed her turned around and faced Rodney.

"Yes, wow you're really into this aren't you?"

"Yes Rodney."

"No I mean you're totally absorbed by this stuff it's so not like you," Rodney said.

"Something for you to think about when you get back," Sheppard countered.

"Goodbye Sheppard," Rodney said solemnly suddenly feeling as if he was abandoning his friend.

"I'll be fine Rodney and I'll see you in a few hours," he said lightheartedly attempting to lighten the mood and failing at it. Rodney left without saying another word to his friend.

"Ready Doctor?" the pilot asked him.

"Yes let's head home." Rodney said slumping down into the copilot seat and closing his eyes trying to relax after several days of grueling research.

"Colonel Sheppard." the AI said.

"Yes Ancient," Sheppard said walking down one of the ships many corridors.

"What have you decided." the AI asked.

"I will stay this ship has much to offer me."

"Good, please head to the medical lab I need to run some tests."

"Ok will this take long because I have to go to Atlantis soon?"

"A few minutes and am I to land on Atlantis?" it asked appearing nearby.

"No they still don't trust you," he informed the AI.

"I understand." A frown appeared on Ancients face however it was soon replaced with a sly smile. "However I am wondering if you will be returning with anyone?"

"Not that I know of although it is possible that Colonel Carter will have someone to accompany me."

"Understood would this be a certain female?" the AI said smugness evident in his voice and his smile.

"I doubt that," he said the thought of the AI looking into his memories thrust into the forefront of his mind again.

"I am in your mind Colonel Sheppard I am aware of certain," Ancient started before being cut off by Sheppard.

"Ok can you stop that?" Sheppard interrupted uncomfortable with the subject.

"It is how I function, that is something you're also aware of."

"What parts of my mind do you have access to?"

"Just your current thought patterns and some of your more passionate emotions."

"That explains a few things," he whispered to himself forgetting the AI heard everything on the ship.

"Like what?"

"Why you knew some things but you seem to be quite wrong about other things."

"Such as."

"Things that would require access to my memories."

"What things have I said that are so incorrect with what you think to be true?"

"It doesn't matter, so what tests are you going to run he said entering the Medical bay."

"Genetics, blood tests, brain activity."

"Genetic testing?"

"Yes."

"Why?"

"Classified."

"The reason for the testing is classified?" Sheppard said becoming nervous at what the AI would do with the test results and why they were even needed in the first place.

The AI furrowed its brow in concentration for a moment before answering, "No just the genetic testing."

"Anyway can you not do it?" Sheppard asked despite the remote chance that the AI would say yes.

"It is required."

"Fine just do it than," he said sitting down on a bed.

After a few minutes he saw the AI appear on a little podium near the office, "Am I done?" he asked it.

"Y_ou are done you may go to Atlantis now," the AI said in his head._

"_You know I don't like you being in my head when it's not necessary."_

"_Yes I am sorry it is a habit I picked up with the former commander of this ship." _

"_So you've told me do I look like him or something?" Sheppard thought. _

"_Yes and I served with him for many years."_

"_How long?"_

"_Several million years."_

"_He lived that long?" _

"_Yes he did."_

"_Is this the one that is still alive?"_

"_Yes, now you must leave immediately if you are to make your meeting and I highly doubt Colonel Carter will look favorably upon tardiness." _

"Goodbye old man,"he said getting up from the bed and heading towards the exit. After exiting the ship he looked around for a jumper and spotted one by the forest he walked over got in one started it up and started flying home. On his way back he reflected on the past few weeks. _I can't believe I never left that ship. At least the bed is comfortable. They'll probably be surprised by some of the things I've learned about the ship. What will they be most surprised with? The Weapons? Shields? Hull? Probably the weapons Rodney can't find where the ships weapons are located but when they find out what the ships weapons are capable of I think they will be impressed hopefully it will be enough to get my request approved. I wonder how much resistance I'll get. It's going to be a big change no more gate travel or anything but hey imagine what I can do we can pick teams up no matter where they are 8 minutes to get anywhere in this galaxy. How long to earth? If only it was bigger than we would be able to carry people between galaxies. But if those weapons he told me about really are really that good than we won't have to worry about the wraith or anyone else._

He continued to fly towards Atlantis however after a few minutes his thoughts drifted once again this time to Teyla._ I wonder how Teyla's doing, could that have been who the AI was talking about? He said he could sense my more passionate emotions are my feelings about Teyla really that obvious? Is he even talking about her or something else entirely? Could he be lying? Does it matter? _So many questions and so few answers he refocused his attention on flying the puddle jumper towards Atlantis. It was still as easy as ever as the jumper did what he thought similar to the ship but not quite as smooth. The ship seemed to know what you wanted before you even asked for it although the mind conversations were pretty weird. After he brought the jumper in for a landing he headed to the medical lab.

When he arrived in the medical bay he sat down and did as the doctor ordered his thoughts drifted again as he sat there waiting for the doctors to pronounce him safe. _No it doesn't she's with someone else not me and she probably never wanted me. But I'll never know now will I. but I shouldn't hold it against her it's my own fault for not doing anything about it, that's my problem not hers. The least I can do is being there for her and the kid. What it's going to happen if we can't find the father and something happens to her? Would the rest of Atlantis take care of the kid or would she want someone specific to take him back to earth and look after him? Maybe I should offer to take her onto the ship she hasn't seen it and she is probably really bored Ronon went off world with other teams and Rodney and I were always on the ship during the last few weeks. Although I'll have to find somewhere to sleep. He thought ignoring the part of his mind saying with her with her with her. _

End Chapter 3

Author's Note- All reviews are appreciated especially critical ones.


	4. Chapter 4

Author's Note- My school had an awesome victory today so I decided to edit this chapter and post it hope you enjoy.

_Chapter 4_

"Ok now that everyone is here," she said looking up at Sheppard who was late to the briefing, "you may proceed with your briefing Rodney."

"Ok now then, we believe that we have determined the location of several Ancient ships," he said looking at Colonel Carter as the screen lit up behind him. "Using the sensor array we believe that there are Ships orbiting these planets," he said as four or five planets lit up on the screen. Continuing with his briefing he looked at Sheppard, "we will be going to this planet because there are no wraith ships in the area and the wraith haven't visited the planet in some time. We have also noticed slight variants in the sensor readings which we believe indicates different classes so we are hoping that this ship will be superior to the Aurora class."

"When are we scheduled to leave?" Sheppard asked looking unconcerned scribbling something on the briefing papers.

"A few hours," Rodney answered.

"Colonel Sheppard you have spent a great deal of time on the ship and are still the only one who can operate it, do you think it's worth it to continue the research?" Colonel Carter asked attempting to draw his attention to the briefing.

"Yes," Sheppard said quickly and forcefully.

"How should we proceed if only you can activate the ship?"

"I'd like to request a transfer to the ship," Sheppard announced still scribbling on the papers.

They all looked at him some with their mouths open shocked at his statement, "WHAT!?" Rodney asked unable to contain himself like the others.

"I'd like to transfer to the ship permanently."

"Colonel Sheppard with all due respect are you feeling ok?" Major Lorne asked him as the others eyed him looking to see if he looked alright.

"Yes I'm fine but that ship is worth a lot even gate travel," Sheppard said slightly annoyed at the insinuation that he was unwell either physically or mentally.

"But it doesn't do anything?" Rodney asked confused.

"Yes it does and if we figure out how to properly use this ship than I'm confident we would be able to defeat the wraith."

"With what the ship doesn't have weapons?" Major Lorne challenged.

Sheppard leaned forward realizing that they were going to make him prove that the ship was important, "Well according to the AI the ship has weapons capable of destroying entire planets."

"Can we trust this AI?" Sam asked the room.

Most of the scientists responded with a no Rodney more adamantly than most, and Sheppard dissented with a yes.

"Colonel Sheppard are you sure you don't want to take some time and reconsider your decision?" Carter asked.

"No, I'm sure this is what I want the ship is definitely worth it."

"I understand I'm placing you on temporary assignment," She said hoping that he wouldn't press her for a more permanent switch.

"I'd like to make it permanent."

"In a few months if you still want to stay on the ship than I'll consider making it permanent," She compromised.

"Ok, see you again in a few months," he said happily turning his attention back to his papers.

"So what have you learned from the ship in your time there?" she asked turning to Rodney and continuing with the briefing.

"The ship is very old but in perfect condition somehow with the exception of how the hull looks."

"How did it look?"

"It was overgrown with plant life when we found it hopefully the ship will clean itself soon I'd hate to be stuck washing the ship," Sheppard said momentarily looking up from the briefing papers.

"Anyway I have no idea what powers the ship or who built it," Rodney continued ignoring Sheppard.

"The AI told me that the builder of the ship was called Ancient," Sheppard told Carter turning his attention once more to briefing papers and drawing something on them again.

"The Ancient's built it?"Rodney asked

"No, the Ancients called the builder Ancient." Sheppard corrected.

"There's an even older race of humans in the universe?" Carter asked leaning forward.

"Apparently, but he won't divulge anything about his creator though."

"Is it a race or person?"

"Single person I think."

McKay continued with his debriefing, "We were able to determine that the ship has highly advanced sensors and shielding, the hull is made of an unknown element, and finally the AI is something that even Ancient ships don't appear to have." Rodney continued on for the next 40 minutes uninterrupted when he finally wrapped up the briefing Sheppard was on the verge of falling asleep and Ronon was asleep.

"Thank you Rodney, Major Lorne since Colonel Sheppard is transferring to the ship you will be taking over his position in the interim."

"Understood Colonel," he said nodding and straightening his papers.

"Rodney, Ronon your mission is being postponed for a few days until another replacement is added to your team," Major Lorne told the pair as Colonel Sheppard nudged Ronon awake and Rodney took a seat next to Carter.

"'Dismissed except you," Colonel Carter said indicating she meant Sheppard. They all filed out of the room while Colonel Sheppard stood up and stretched.

"Colonel I was wondering why you suddenly chose to stop going through the gate?"

"It's the ship Colonel Carter it's very important if I can learn to control it then we can really give the wraith a hard time" he could tell she didn't buy it but what else was he going to say?

"Colonel I'd just like to make sure that you're not doing this to avoid replacing Teyla."

"I'm not," he said defensively.

"Then there's one more thing I'd like to ask you."

"What's that?"

"Well Teyla has seemed pretty bored around here and I'd like you to take her with you."

"Ok I'll ask her," he said as he turned and left for Teyla's quarters smiling that he had didn't need Colonel Carter's permission to bring Teyla.

He waited outside her quarters activating the door chime twice. When he tried a third time however when she still didn't answer he decided that she might not have been in or she didn't want to talk to him. So he turned to leave when the door opened.

"Colonel Sheppard," Teyla greeted him and motioned for him to enter.

"I'm off duty you can call me John," he said.

"Of course John, have you made a decision regarding me rejoining the team?" she said as she sat on the bed and indicated that Colonel Sheppard could do the same however he remained standing wanting to keep a comfortable distance between themselves.

"It's not up to me anymore," he informed her looking down and digging his hands into his pockets.

"Then who?" she asked confused.

"Whoever is running the team probably Major Lorne," he said raising his head to stare into her eyes.

"Why will you not be running the team, have you been promoted?" she asked surprised that he would leave his team and figuring that the only possible reason being that he was being sent back to Earth or that he was promoted out of the field. But would he not have told her if he was going to be forced to leave. _Could he be getting back at me for not telling him I was pregnant? Why would he do such a thing?_ _Perhaps there is another reason why but what? _

Noticing that her brow remained furrowed John hurriedly explained, "No I transferred to the ship that we recovered."

"Why," she said shock evident on her face.

"It's important and I was wondering if you would like to uh… well join me on the ship?" he said pausing before continuing, "you seemed pretty bored and I thought you might like a distraction," he said very quickly trying to explain himself.

"If Doctor Keller thinks it will be ok I will join you" she said a little uncomfortably and giving him a meek smile.

"Great I'll tell Carter," he said before leaving her quarters.

"John," she said as he entered the hallway.

He spun around, "yes Teyla."

"Thank you," she said, he gave her a sly smile and left.

End Chapter 4

Author's Note- All reviews are appreciated especially critical ones.


	5. Chapter 5

Authors Note- Thanks for the reviews I will be updating with the next chapter tomorrow as it is my favorite one so far.

Start Chapter 5

Sheppard sat in the infirmary waiting for Keller to finish her tests when Colonel Carter walked in and motioned for Keller to come over when she got to Carter she whispered something to her and left. Keller than walked back to John, "So I'm told that you're not coming back for a couple months is that right?"

"Yup unless Teyla wants to come back to Atlantis."

"Well I'm going to be running a few extra scans then, head over to the scanner," She instructed, he got up and did as he was told.

"So doc anything wrong with me," he asked after the machine had finished.

"No you're fine," She said sadly realizing that there were no traces of an alien influence although his endorphins were slightly elevated but there were so many possible causes for that.

"Thanks doc," he said jumping off the table and jogging out of the infirmary. Keller touched her earpiece and called Carter.

"So what did the scan turn up?"

"Nothing at all," she said sadly.

"Are you sure?"

"Yes there is nothing physically wrong with Colonel Sheppard that I can find, I guess he actually wants to go on the ship."

"Could the AI have done something? Sheppard avoided mentioning how it interacted with personnel and it seemed to know a lot about him."

"Well if the ship is manipulating his mind I can't detect it."

"Scary thought," Carter said as a chill made its way up her spine as she thought about possible consequences if the AI could manipulate minds with no traces what else could it do? Could it get someone to sabotage Atlantis? They definitely needed to learn more about the ship but the only way to do that involved sending personnel onto the ship.

"But I have no way to prove it," Keller finished sitting down in her office and beginning to file the paperwork on the Colonel and Teyla.

"Did you run the scans on Teyla yet?"

"She's clean as well although I'd like her back here next month."

"I'll tell them before they leave," Carter said turning off her headset and getting back to the pile of paperwork on her desk.

Sheppard waited outside Teyla's quarters he went to activate the door chime again when the door slide open, "Teyla are you ready?" he asked her.

"Yes, I think so, doctor Keller has requested that I return next month"

"Ok let's go," he said picking up her bags and heading to the jumper.

After entering the jumper she sat in the copilot seat after several minutes of flying neither of them had said a word. Finally Sheppard attempted to break the silence, "So what have you and Ronon been doing while Rodney and I were on the ship?"

"Ronon went on missions with other teams, and I monitored the search for my people," she said before the heavy silence once again descended.

"Are you interested in seeing the ship?" Sheppard asked after a few minutes hoping that this would get her to talk he felt as if they hadn't had time to talk to her in a long time.

"Yes I think it will be a very interesting experience."

"What do you know about the ship?" he asked her still trying to get the conversation to stick.

"Not much I did not attend the briefing or read the reports."

"Well it's small but fast and apparently pretty powerful, the AI is very good he sent me breakfast."

"How did it know how to make the food?"

"It probably pulled it," he said pausing when he realized what he was going to say, "Bastard lied to me he does go into my memories."

"The AI is aware of your memories how?" Teyla asked clearly alarmed and nervous.

"Don't worry he's only entered my mind so far but he can read minds."

"Does Colonel Carter know about this?"

"I think so I'm sure I mentioned it to Rodney and he probably told her."

"So she might not be aware, is this not a security risk?" She asked despite knowing what the answer.

"Well yeah I guess but he said that he doesn't look at people's memories," he turned to her his gaze intense which she met and held. He covered her hand with his, "And he won't hurt us."

""Why are you so sure?" She turned her head and faced out the front window again.

"He just wouldn't he has no reason to," he said however she never responded because the ship came into view.

Following her line of vision he saw the ship come into view, "The ship is beautiful John."

"Yeah it wasn't that good when I got on it," he said noticing that the ship seemed to have become sleeker and newer it was no longer covered in vines and the grime that resulted from sitting on a planet for 10,000 years it was glistening in the early morning sunlight the ships itself appeared to be a light blue or silver. Sheppard was now able to make out the different parts of the ship and noticed several strange pieces of design on the ship. They quickly landed and entered the ship.

"John is there anything you need me to do."

"No you can relax I'll be in the command room for a few minutes and then I'm going to head to a new room and learn what it does."

"Can you show me where I will be sleeping?"

"Yeah sure, AI can you activate," he said heading down a hallway.

"Yes Sheppard oh I see you have brought someone with you," it said appearing nearby in his usual two foot form and smiling at him.

"Yes I just need to take her to the bedroom and then I'll be in the command center is there any way she can gain access to the ship?" he said despite knowing the AI would say no.

"I shall see to it that the ships systems become available to her," Sheppard's eyes went wide and he stopped in the middle of the hallway.

"What really, why didn't you do that for Rodney?" Sheppard sputtered shocked that the AI would allow her access to the systems.

"I did not think he was trustworthy."

"Thank you AI," Teyla said sweetly smiling nervously at Ancient.

"Call me Ancient or old man as Sheppard prefers," he said showing annoyance at the latter term.

"You were constructed by the ancestors then?"

"No my construction predates the ones you call ancestors existence."

"Who built you?"Teyla asked as Sheppard looked at her and smiled at her. She had no idea how hard it could be to get simple information out of the AI.

"His name was ancient which was then passed on to me."

Why was he called just ancient?"

"No but I cannot say what his other names are."

"After John shows you his bedroom I need you to go to the infirmary there are some tests I must run."

"I thought I was to have my own room Colonel?" she said turning to Colonel Sheppard and eying him questioningly.

"You are, there's only one on the ship and so that's where you will be sleeping."

"Oh thank you John."

"Here we go," he said opening a door and showing her into the spacious bedroom, "Good?"

"Yes John, "Teyla said moving around and admiring the room she eventually wandered over to the window and stared out of it. He moved next to her admiring the view.

"So what do you think so far?"

"The AI is interesting but you should have told Colonel Carter about the AI reading minds."

"Don't worry you won't notice it."

"The AI will be probing my mind?"

"Yes it's how it interacts with personnel," He said.

"You did not tell me that John," she said a hint of anger seeping into her voice.

"Sorry I guess I just forgot it's not really that noticeable."

"You did not even ask me if I wanted the AI to interact with me."

"Look I'm sorry Teyla but don't you want to be able to interact with the ship?"

"That is not the point John."

"Then what is the point?"

"That you did not ask me if I wanted the AI to enter into my mind. We do not know if there are any effects of it doing so."

"I hate to interrupt your fight but I need you in the medical bay Teyla," Ancient interjected appearing between the two.

"Follow me Teyla," he said leaving. She followed in silence.

After arriving John left saying he was going to give Teyla some privacy and that he would be in the command center should she need anything. After he left the AI spoke to Teyla.

"Please sit on the table," The AI said appearing next to one of the scattered scanner beds.

"What kind of tests will you be running?" she asked the AI nervously.

"Simple blood, DNA, a few others don't worry none will harm you."

"And none will harm my child I assume?"

"Congratulations I'm sure you and John shall be very happy."

"John and I are not together," She informed the AI as she laid back on the bed.

The AI froze for a few minutes stunned by the revelation after a few minutes the AI regained his composure, "Oh," the AI said surprised by this revelation.

"What gave you the idea that we were?"

"You both showed up together there is only one bed in the entire ship I simply assumed that you would be together."

"We are not the father's name is Kanaan."

"Lie down and relax the scanner will be done in a few minutes," the AI said before disappearing. After finishing the AI told Teyla that it would enter her mind slowly and that she would notice the ship starting to respond to her soon. He also mentioned that it was possible John and Teyla might have some sharing of thoughts and in extreme cases emotions.

"Where is John?"

"Research lab 2, take a left then a right and it will be the fourth door on your left."

"Thank you."

"You and Teyla are not together?" the AI said appearing on a pedestal next to Sheppard.

"No why would you think we were?"

"Why is she here if you are not together?"

"She's a friend of mine who was pretty bored so I thought she might like to come here."

"If you are not together would it not possibly be awkward when you share the same bed?" Sheppard opened his mouth to say something however Ancient cut him off, "I saw what you were thinking about when you brought her into your room and I don't think you would be able to entirely restrain yourself."

"We are not going to be sleeping together," Sheppard said moving away from his current console and onto another nearby one.

"You are aware that there are no other beds on this ship," It said watching Sheppard move around the room away from the pedestal.

"Yes I will be sleeping on the bridge," he said pressing a few buttons and attempting to ignore the AI as best he could.

"Of course," The AI said his voice sounding skeptical while his image appeared confused except for a small smile that Sheppard didn't catch.

Authors Note- All reviews are appreciated.


	6. Chapter 6

Authors Note- this my favorite chapter so far and the last update until I finish writing chapter 14 which could take a little while as I'm still on chapter 9.

End Chapter 6

Teyla had attempted to follow the AI's instructions but the ship was quite confusing it had been several minutes since she had left the infirmary. When she tried to return to the infirmary however she was unable to return and when she entered the room she thought was the medical bay she was surprised to see several consoles arrayed around the room forming a semicircle. Across the room she saw an object similar to the one that she remembered had held an old doctor weir during her first year on Atlantis. Deciding that she should ascertain the purpose of the room she attempted to activate a nearby console. It stayed on for a few seconds before it died without warning, "strange McKay said that the ship had ample power and John had never mentioned any problems."

"That is because they never attempted to enter this room," The AI said from somewhere behind her however when she turned around to face him he was not on his usual pedestal or a disembodied voice but he appeared as a fully grown human albeit a blue glowing one. It slowly ambled around the room eying her. She found herself unable to move from the spot as it stood face to face with her with her. She knew that she needed to move that she wasn't wanted here but she stood frozen at the spot from a combination of fear and awe. The AI reached over to the console she was standing at touched a few buttons on it as she simply stared at it wondering if it was actually there or not it looked like it had touched the buttons but still appeared a tint of translucent blue.

It read her mind and responded out loud in a hushed voice, "No I am not physically here I have no physical body," the AI said its eyes still fixated on hers its voice icy cold without any emotion. The former kindness completely absent from both its demeanor and voice as it stood less then a foot away from her.

"What are you doing, how are you in this form?" she asked trying and failing to keep the fear she felt from her voice. She tried to move away from the AI which was still staring menacingly at her however when she stepped back the AI stepped forward and she was soon backed against the wall. Her eyes darted around the room looking for something anything to distract herself from the thing that stood in front of her. The AI stood there for a few minutes searching its databanks for information.

After finding what it needed it spoke to her again, "You should have followed my instructions, you are not allowed in this room."

"I…I thought we had full access to the ship?" she said attempting to move again but finding her body unwilling to obey her minds commands.

"No one has access to this room I would recommend that you leave immediately," It said as its lips formed a cruel smile.

_It can't actually hurt me can it? No it said it has no physical body. _She thought before the AI intruded fully into her mind for the first time.

"_But I control the ship," the AI said in her head. The AI then proceeded to implant the information it had found in its databanks into her mind which contained some of its most horrific memories of both past and future events. _

At hearing the AI in her head her body finally moved she quickly made for the exit of the room afraid of what the AI could or would do. When she stepped into the door frame a bright light washed over her erasing her memory of the events that had just transpired and activating the memories that the AI had put into her mind. After exiting the room the door shut behind her promptly she leaned back against it and let out a deep breath and began crying. She sank to the floor and put her head in her hands and sat there until the AI called her to the infirmary. At hearing the voice of the AI she activated her comm. and called John she was afraid of the AI but didn't know why and the images were very painful she needed someone to comfort her. She had a suspicion the AI had something to do with them as she had no other explanation for why she should see so much death and destruction now when she was on this ship with John of all people.

"John are you there?" she whispered into her comm.

"What's up Teyla?" he asked nonchalantly although he was concerned about what was wrong with her.

"John are you ok?" she asked ignoring his question.

"Yeah Teyla what's wrong?" he asked his concern continuing to grow as she evaded answering his question he had never heard her sound like she did now.

"I am now able to exert some control over this ship," she said quietly evading his question again.

"Teyla where are you I'm coming to get you," He said.

"I do not know John I…I was coming to find you but I got lost and the AI," she said before breaking down and taking off her comm.

"I'll be there in a minute," he said before turning on the AI.

"WHAT DID YOU DO TO HER," he screamed scaring the AI.

Visibly shaken the AI quickly responded, "Nothing I have no idea what is wrong with her," The AI lied.

"Show me where she is NOW."

"Here," the AI quickly responded bringing up a map with a dot showing where Teyla was. Sheppard immediately sprinted towards her location. After about two minutes he reached her when he turned the corner he was surprised to see her curled up against a door head in her hands. He moved over to her and sat down next to her. He brought her closer to him and she pulled him into a friendly hug. He returned the hug and waited for her to stop crying. She finally stopped and pulled back although she remained sitting against the door and close to John.

"Teyla what happened?" He asked when he thought she had recovered enough to answer a few simple questions.

"I do not know John, I have these images in my head and...," her voice trailed off and she looked down again as she struggled not to begin crying again.

"Of what Teyla I can't help you if you don't tell me."

"Kanan, the Athosians, Atlantis, Ronon, others I do not know, and you."

"What about us." He asked putting his arm around her.

"You are all being tortured and killed among other things and I am forced to sit and watch and in one case participate."

"Teyla it's not real, I don't know why you're thinking about these things but there not real and there not happening," He said knowing that what he said didn't really matter she would be thinking about these things for the time being the most he could hope to do was to distract her for a few minutes. He often had similar dreams about Afghanistan although Teyla's seemed much worse than whatever he had ever suffered through.

"Yes John but still I see them and…," once again her voice trailed off and John brought her into another hug attempting to comfort her.

"Do you think you can stand?" he asked after the much briefer hug.

"Yes John I will be fine," she said being embarrassed at how weak she must look something she did not want.  
"Come on then the AI needs us in the infirmary," he said helping her to stand up. He helped walk her to the infirmary still worried about her.

When they arrived he noticed that the AI eyed her strangely but then changed back to its normal demeanor.

"What do you need her for?" he asked the AI as Teyla sat on the bed near the door.

"I would like to run some tests," it responded weakly.

"Did you not already do so?" Teyla asked.

"These are different tests on the baby."

"Oh do I need to leave?" John asked slightly embarrassed.

"No stay John," she told him not wanting to be left alone with the AI she still had the suspicion that he had done something to her to give her those visions.

"Ancient would it be inappropriate for me to stay?"

"No."

"Ok Teyla I'll stay," he said reaching out and grabbing her hand as another light washed over her.

Authors Note- All reviews are appreciated.


	7. Chapter 7

A/N- Sorry about taking so long to update I've actually had this ready and perfect for a few months but just neglected to update. Since it could be a little while before I update again I apologize however I must certainly have not given up on this story and don't intend to. I'm currently writing chapter 25 and the story should finish somewhere between 50,000 and 60,000 words. I will try to update as soon as I get chapters back from TRECEBO.

Thank you TRECEBO for this chapters beta.

The space gate activated and two jumpers flew through, scanning the area as they exited. They quickly located the ship in orbit around one of the planet's two tiny moons. "What do have McKay another Aurora?"

"No judging by the landing bays it looks like we've got us a big empty carrier," he watched the scans waiting for any sign of nearby wraith.

"So do we want it or not?"

"Yeah just land inside one of the bays you shouldn't have anything to interfere with it the bays are empty of fighters."

The jumpers slowly flew into the hangers; they noticed that the entire ship appeared deserted not a single spare part for a fighter. There was no equipment strew about; it looked like the Ancients had just left the ship. Scans showed there was no breathable atmosphere.

Major Lorne looked back at the scientists, Rodney in particular. "Well, someone is going to have to go out there and reactivate life support systems."

"What? Why me?" McKay gestured towards a scientist whose name escaped him. "Why not him?"

"Because _you _actually know how to turn on the system and have some experience doing this stuff--unlike Doctor Dyer." Lorne pinned him with a stare.

"Oh, fine! You're worse than Sheppard," he grumbled under his breath, exiting the jumper and heading out to the controls. After studying the controls for a moment, Rodney managed to get the fighter bay shield up and reactivate life support. "There. Happy now?"

Leaving the fighter bay, the two teams headed to the bridge. Upon their arrival, the ship's systems sprang to life and Rodney went to work determining what happened to the ship.

Half an hour later, Major Lorne returned to the bridge, his team unable to find any clues about the ship. "Doctor McKay?"

"Yes, yes," he said, tapping a few buttons on the tablet connected to an ancient console.

"Do you know what happened to this ship?"

"Yes, well, it looks like the ship's weapons systems are for defense only. The ship itself is supposed to jump in, launching its fighters, then retreat with others of its class, using planets, moons, or the Ancient fleets as protection from the Wraith. The fighters would then engage the Wraith darts much like our F-302s."

Lorne rolled his hand in a 'what next?' kind of motion. "And..."

"Well, they had launched all of their fighters, as we can see here," Rodney pointed to the tablet data, "when a pair of Wraith cruisers broke off from the main fight, and headed towards the carrier group."

"So, what? The Ancients just abandoned the ship?" The major raised a skeptical brow.

McKay paced next to the console. "Yes. _This_ ship appears to be the flag ship. The Ancients probably abandoned it when the cruisers approached the Ancient carriers."

Now Lorne frowned. "Are you telling me all of those carriers couldn't take on two wraith cruisers?"

"No, they could have-- and probably did--but the Wraith would have signaled for more ships to follow. The Ancient carriers would be able to take out a hive or two, but they would sustain losses and they didn't want to risk _this_ ship being one of the losses. Their whole high command would have been killed in one attack." With a grin, McKay pronounced, "This ship was part of the largest Ancient fleet."

"Why didn't the wraith know where the ships went after they launched their fighters?" Striding to the command chair, Lorne gave it a once over.

Rodney ignored his movement, intent on finishing his information. "These ships are designed to be stealthy. There is cloaking device, but I don't know how well it works."

Signing, the major took a seat, surprised as it lit up. He noted McKay's preoccupation. "So, the ship isn't as good as an Aurora?"

"Well, not one-on-one, but if we fill it with F-302s, it can be useful if we need to take out, say, a hiveship's complement of darts or attack a hive ship itself. We could theoretically jump in-system undetected and launch our fighters against wraith ground installations or attack darts that are culling a planet."

Lorne leaned back in the chair, his ATA gene doing its job. "Any chance of finding the missing fighters?"

"No." McKay sounded gloomy as he continued working on his console.

"How about activating the hyperdrive?"

"How did you--" McKay said before realizing that Lorne found an active control chair, and knew which systems were online and which ones were offline. "In a few hours, I should have them up." He moved around to different consoles, attempting to get more information on the ship, and to determine where best to send repair teams.

The major squinted at a screen. "Any chance of speeding that up?"

"What's the rush?" Slightly annoyed, McKay continued hurrying from one display to the next.

"I'm picking up some wraith ships nearby."

"How close?" Stopping cold, Rodney feared he would once again be forced to complete some task and save the day with about 10 seconds to spare.

Lorne took pity on the scientist. "About an hour--maybe two-- assuming they decide to cull this planet."

Pulling up local data, McKay grimaced. "Well, the population is pretty small. Hopefully, they don't decide that this place would make a good snack."

Lorne craned his head to look at the man. "I'd rather not risk everything on the Wraith not attacking this planet."

All business now, Rodney grabbed his laptop. "Ok, let's get the hyperdrive back online, shall we?"

"I'll let you know if the Wraith head toward us," replied the major as McKay left to begin repairs.

A little under the prescribed two hours later, Lorne focused on the forward displays. "McKay, are you sure they're not going to just blow us out of the sky?"

"Yes, yes, look we don't have much of a choice." Rodney scrambled from one panel to another, still punching in code. "There was no way I would have been able to get them online before they got here. The damage was greater than I thought."

"But we're just sitting here. Shouldn't we prepare to open fire?" The approaching ships drew closer than the major liked.

"We need to test the cloaking technology. If it works, then the Wraith should just leave; if it doesn't, then we run, and hope I can get the hyperdrive online in time," he mumbled to himself as he raced to fix said hyperdrive.

"And weapons?" A fully stocked supply of drones had been found.

"Online, but don't shoot too early."

"I won't." Lorne sounded confident.

McKay activated the ship wide comm, "Ok, everyone...we are going to activate the ship's cloaking device. Please power down everything you're doing."

"Detecting hyper space window,"called one of the technicians.

No one said anything for several minutes, the only sound in the room coming from Rodney tapping on his keyboard. Finally, he spoke in a hushed tone. "Looks like they didn't detect us."

Major Lorne hissed back, "So, the cloak is working?"

"Well, we're still alive, aren't we?" McKay couldn't pass up the sarcasm.

Lorne met his gaze. "I don't want to stick around. If you wouldn't mind, get the hyperdrive back online."

"What are they waiting for?" Lorne asked McKay. The Wraith ship had simply exited hyperspace and gone into orbit nearby.

Rodney pulled a face. "Do I look like I--wait, they're turning."

"I see that."

"But they're turning right for us! They might detect us."

Rolling his eyes with shortened patience, Lorne ground out, "I thought you said they couldn't detect us?"

"Well, they shouldn't, but they might. They had to have found the carriers somehow in the first place." Rodney tweaked the cloaking controls gently.

"Did they detect us?"

"They aren't shooting yet."

"They're moving off, McKay," Lorne released the breath he hadn't realized he had been holding.

The Lantean carrier exited hyper-space above Atlantis. "Colonel Carter, this is Major Lorne. Do you read us?"

"Yes, Major." Carter looked at the heads-up display. "How is the ship?"

"The stealth systems work for the most part--unless the wraith scan our immediate area, we'll be safe."

"That's good to hear. What kind of ship is it?" She watched information scroll by on her laptop.

"Transport carrier class. It doesn't do well in a fight." He tried not to look disappointed.

Carter crossed her fingers. "Any fighters onboard?"

"No, ma'am. And McKay says chances of finding any are slim to none."

She could see Rodney in the background, complaining. "How many F-302s do you think it will hold?"

"A lot--I'd say at least four or five times more than the Daedalus."

"Well done, Major. SGA teams 3 and 4 are returning with an Ancient battleship so perhaps we can find use for it there."

Surprise colored the major's voice. "You said SGA 3 and 4 are bringing back a battleship. Aurora Class?"

"Better, I'm told," she smiled.

He returned the gesture. "Good. Where do you want us to leave the ship?"

"In orbit around the planet for now. We're going to need to work out somewhere to store the ships in the long term." She sent a set of coordinates up to the ship.

As the ship took up geosynchronous orbit, Carter turned towards the gate and the three jumpers waiting. "SGA teams 5, 6, and 7, you are clear to go, and good luck."

She watched first jumper descend and go through the gate. Once the event horizon closed, the second jumper dialed new coordinates, following the same protcol as the the previous. After the final jumper went through, Carter smiled to herself.

So many years after they had first gone through the gate and alerted the Goa'uld to Earth, they were finally getting a fleet of warships to defend themselves, and fight back against the Wraith and the Ori.

_End Chapter 7_

A/N- Reviews are always appreciated


	8. Chapter 8

_End Chapter 7_

I haven't abandoned this story it's actually about 95% done at this point. Unbeated sorry.

A/N _italics _either mean mental conversation or first person thoughts I've attempted to remove most of the first person thoughts however some will still remain.

Ancient acts according to his own agenda so he won't be evil unless it suits his agenda I'll try and find somewhere for him to be a bit more evil in the future. And also it will be a very long time until his actions in 6 are explained.

_Chapter 8 _

"Ok that is all you may leave," the AI told John and Teyla as he disappeared from his pedestal.

"Do you have anything to help Teyla?"

"Actually I already administered a suppressant for the memories, I don't know where she accessed them but they were not meant for her mind."

"What are you going to do?" John asked Teyla still holding her hand.

"I think I will join you for a few minutes until I retire," she said sitting up and removing her hand from Johns.

"Ok this way," he stopped and waited as she got up from the bed. "Do you remember where your bedroom is?"

"I believe so," She said distantly.

"Well if you need me to I'll walk you back there," they walked out the door.

She gave him a weak smile, "I do not think that will be necessary John."

"Are you sure?"

"Yes, you can escort me back if you feel it necessary," she offered hoping to ease his concerns.

"No, no I'm sure you can make it back on your own," he said diverting his gaze away from Teyla and towards the wall.

Deciding to change the subject she wondered what they would be doing for the next few months, "What are we going to do now?"

"Follow me," he said turning to the door and exiting the room.

They entered into the room a few minutes later and John immediately went to the console he had left when he went searching for Teyla. He started pressing buttons and bringing up screens again. He began the slow arduous process of translating the text in an attempt to learn what was stored on the computer. Teyla went to a nearby console and proceeded to do the same.

"John what does this mean?" she said upon coming to a word that she did not have a translation for. He walked over to her screen and joined her in the circular raised platform standing close to her.

"Hmmm I think that means," he said before pausing looking back at his book and then looking back up at the screen several times, "it means plane of existence."

"As in where the ancients reside now," she commented reading through the rest of the passage.

"That's just it I don't know in the context it doesn't make sense its talking about some sort of war on what they refer to as the high or highest plane."

"Perhaps it is the Ori that the ancients were fighting."

He gave one last look at the screen, "I guess I just didn't know that they ever actually fought with each other."

"Thank you John," she said stepping away from the console in order to get some space between them.

"Happy to help," He stepped off of the console as well.

"I think I will retire now," she said yawing.

"Are you sure you know the way back?" his concern for her surfacing once again.

"I will be fine however if it will put you at ease you can escort me to your bedroom."

He considered walking her back for a moment but decided that he shouldn't because she clearly didn't want him to besides if he walked her there he knew that he wouldn't want to leave hell he didn't want to let her walk to her bedroom alone how would he feel knowing that she was sleeping when she had been through something so horrible she was unable to adequately describe it but a scant few hours before. He'd had enough trouble letting her go to bed alone during the past few years even when he knew she would be able to shrug off the devastation they saw every day. Knowing that things weren't ok he didn't know if he could let her go alone to face the possible nightmares. As he looked at Teyla he noticed two things one she was blushing slightly probably due to the fact that he had been staring at her and was making her uncomfortable and two she was looking at him strangely. It took him a second to realize that he hadn't said anything in awhile and that he should probably respond to her, "No I'm sure you'll be fine," he hoped that the memory suppressant worked on her dreams as well.

She turned to him as the doors parted, "Goodnight John."

"Goodnight Teyla," he watched as she walked out of the room the door closing silently behind her. He turned off her console and headed back to the one he had been working on.

* * *

After a half an hour of working the AI appeared on a pedestal next to Sheppard.

"Hello again Colonel Sheppard," it said positively beaming at him.

"Activate the security cameras outside the bedroom," he ordered dryly.

"I have felt your emotions for her and I have seen how you two have interacted since you first met why have you never attempted to move your relationship with her beyond friendship?" Ancient asked ignoring Sheppard's order.

"Does it matter?"

"Yes," he said

"Why?"

"Because I must know why you have not told Teyla how you feel, it could cause you to feel strange if she discovers how you feel and did not reciprocate."

"How would she discover how I feel about her?" he suddenly became very concerned that Ancient might consider telling her for whatever reason.

"Well it is possible that because your minds are both connected to the ship that you could share thoughts, memories, and emotions."

"So you're saying that she will eventually sense how I feel about her?"

"It is possible that she will and given the strength…"

Sheppard cutoff Ancient, "I don't need you reminding me about my emotions I realized how I felt about her years ago."

He smiled, "Yet you never told her."

"There was never time and besides she doesn't feel the same way about me." He said sadly lowering his head as the final words escaped his lips.

"Why are you so sure?"

"Well for one she's pregnant with another man's child," he slumped down into the chair he was sitting on.

"So have you not been with women despite your feelings towards her?" he asked coldly taking no pleasure in what he was baiting Sheppard into.

"No I haven't," Sheppard said putting no conviction behind his words.

"Oh really?" Ancient said raising one of his eyebrows.

"Not in the same way she was besides that was one person years ago she's been dating this guy," he said with emphasis on his last statement and sat up in the chair becoming alert again.

"Then why has she never mentioned him to you?" John stood up out of the chair.

"I don't," he started before pausing "How did you know that she never mentioned him? How did you know how to make me my favorite breakfast? How did you that I never told her how I felt? You lied to me didn't you?" He demanded advancing on him angrily.

"Yes, I did not wish to scare you I have not and will not do the same to Teyla," It said quickly as Sheppard towered over him.

"Oh and why should I trust you now after you lied to me and I've got a feeling you hurt Teyla in some way," Sheppard said keeping his voice just below screaming incase Teyla had gotten lost and was coming back.

"John I may have manipulated you lied to you and done a few other things but it is all for your own good," The AI said as it pulsed a much darker shade of blue.

"Teyla is leaving," he said defiantly as he headed for the exit and Teyla.

"She is safe here and she should be here with you, trust me John," Ancient begged closing the door in front of Sheppard trapping him.

"Let me out," he said looking angrily over at Ancient.

"When we finish this conversation I will happily let you leave."

"Fine why do you want her here?"

"Because you love her and she should be with you," Ancient said desperately hoping to use John's own emotions against him.

"And you would care about how I feel about her why?"

It turned and smiled at him, "Does it matter?"

"Yes it does for all I know you're going to mess with her mind," Sheppard angrily paced back and forth across the room.

"I simply wish for you and Teyla to be happy."

"Well unfortunately those goals are mutually exclusive," Sheppard said heading towards another exit attempting to get out again.

His smile dropped, "How so?"

"Teyla wants to be with Kanaan and I want to be with Teyla."

"What makes you think that Teyla would only be happy with Kanaan and you only happy with Teyla?"

"It's logical to assume that Teyla wants to be with the father of her child," he said trying the final exit out of the room which was also locked.

"John is it so impossibly inconceivable to believe that perhaps Teyla wouldn't hate being with you?"

He turned back towards the wall before responding, "Yes it is," he snarled hating the words he felt forced to say just to argue.

"It is in fact conceivably possible that she could fall in love with you," he said as Sheppard returned to the center of the room.

"You're not going to mess with her mind to make her fall in love with me are you?" the accusation stung the AI causing him to cringe.

"No I would never do such a thing," Ancient's voice became much more subdued as he now knew he had Sheppard beaten.

"I've heard that before," he noted snidely.

"I would not lie to you about her," he said releasing all of the doors allowing Sheppard to exit.

"And what happens when you realize that she is already in love with another man and she doesn't want me as anything more than a friend?"

Ancient's eyes fixed with Sheppard's, "That will not happen," he said his voice deadly serious.

Despite trusting the AI again he still didn't believe Ancient could possibly succeed, "Let's say it does."

"Nothing except I will have failed for the first time in my very long life."

Sheppard smiled slyly at him, "You must not take many risks then."

"On the contrary I take many and they _**always**_ pay off," he said smiling himself.

"You must be really lucky then," he said as a smile spread across his face.

"Very," Ancient said smiling as Sheppard relaxed for the first time since Teyla had called him over the radio earlier that day.

_

* * *

_

_Good the first phase is complete now If I can just need to get Teyla to fall in love with him, I hope she really does have those long hidden feelings that would make things so much easier. What I'd do for the good old days when all I had to do was wipe out a couple fleets of hiveships and call it a day now I've got to get two people to fall in love in the span of a few weeks and hope that the others continue my work after I'm forced to leave._

He snorted at that though,_ Yeah like the others will help they haven't helped in ten thousand years and even then help was sporadic at best but Ancient always told me to have some faith that in the end no one can stand by and watch as those you care about are slaughtered not even them. And even if it works I'm still going to get purged for putting words into his mouth, merging thoughts, showing Teyla those things, and of course the regular mind manipulation. Well at least I will have succeeded perhaps Teyla will understand Sheppard most certainly won't, he_ thought before powering down for the night.

_End Chapter 8_

A/N all reviews are appreciated thank you.


	9. Chapter 9

_Chapter 9_

_A/N Well I just finished up the story with the exception of rewriting and editing which still needs to be done on all chapters. It is 32 chapters and around 67,000 words just to give you an idea of how much is left. _

_Numbers and equations indicate ship operations_

Sheppard stood outside the bedroom contemplating whether he should enter or not. He hoped that she was still asleep if she was getting changed that would be well awkward; deciding that he couldn't wait outside the room for her to emerge at whatever hour he approached the door one last time and activated it. It slid open silently and not wanting to wake her he quietly entered the room. As he slowly made his way toward the bed he admired how peaceful she looked as if there were no wraith or Genii or anyone else who wanted to kill them. He breathed deeply relishing the moment. It was moments like this that made him realize how much he did love her and how much he wished for more of those moments. It was something only she had been able to do even while watching over his team members Rodney simply caused those worries to jump to the forefront of his mind as he was the one who usually complained about them. Ronon showed him how hard they fought how far not only Atlantis but everyone in Pegasus was willing to go but it was Teyla who showed him why he fought. As he watched her he noticed that while she was resting very peacefully now it appeared that her night had not been so peaceful. As he sat there contemplating waking she mumbled something he couldn't understand. Knowing that she could wake up any moment and see him just staring at her he sat on the bed and gently laid a hand on her shoulder, "Teyla sweetheart wake up."

_Did I just call her sweetheart where did that come from?_ John felt something in the back of his mind. It was foreign, certainly not something he normally felt._ Could it be him influencing me? He is so dead the second I figure out how to kill him._ He remembered his conversation the previous night and winced as he realized it could be Teyla in his mind now._ I hope she didn't hear me say that. What happens if she did hear me? _His train of thought was quickly interrupted when she opened her eyes and smiled at him, "Good morning," she said softly while unconsciously snuggling closer to him.

He returned her smile although he was slightly confused by it, "What's got you so smiley this morning?"

"Mmm well," she started before she started to realize who she was talking to, "John?" she asked blinking furiously as the smile disappearing from her face.

"Expecting someone else here?" he joked as he tried to hide his own disappointment by looking away from her.

"I'm sorry John but why are you here?" she asked her smile weakly returning.

"Well I wanted to check on you and the old man thought it would be a good idea."

"I assure you I am fine John," she said slowly moving away from him when a thought entered her mind, _"Dodged that bullet I'm glad she didn't hear me call her sweetheart." _

"John?" she asked with a grave seriousness in her voice.

"Yes Teyla," he said becoming nervous by the change in her tone. _Did she actually hear me call her sweetheart? Oh no wait the AI said thought could she have heard my thought way to go John you just told her what you did._

His attention returned to Teyla when he realized she was speaking to him, _"_John did you call me sweetheart?"

_It's now or never I could lie to her tell her no unless she did actually hear me and if she didn't then she's probably hearing this thought to and would know I'm lying to her but what else does she know? _"Yes I did," he said hanging his head low figuring that this was the end of their friendship she would inevitably ask why to which he'd have to reply that he loved her. And that would lead to awkwardness in the past he could have hoped she'd tell him she felt the same but she was with Kanaan now and while there was still a small spark of hope in him, that said that maybe just maybe all those moments throughout the years hadn't been imagined, maybe she does care for me more than a friend; the logical part of his brain told him that wasn't possible she would have responded to some of his advances or made some of her own. Sure his advances had been subtle so subtle that whenever she said no he brushed it off figuring she didn't understand what he was really asking but now he knew she did know she just didn't care about him in that way. But that was something he preferred to just not think about and shove down deep into a dark corner. He slowly raised his head to look at Teyla again the sadness he felt written across his face but he didn't care if she saw what she could do to him with one question he loved that about her she could change his entire day, week, month, year, even life with but a single word or even just a look. Admitting and learning that piece of information however had not been easy and he'd never

"John among your people what does that signify?"

"Well uh yeah umm… about that do you uh mean that you don't know what it errr well know what it means?"

She looked at him puzzled by his sudden discomfort, "I have heard the term used in Atlantis but I do not understand the context of the way you are using it."

"Colonel Sheppard please report to the command center," Ancient interrupted to Teyla's disappointment and John's visible relief. "_Thank you Ancient," _he thought to Ancient as he got up and headed to the door Teyla followed behind him.

"May I join you?"

He turned around and looked her up and down, "uh don't you want to get changed first?"

"Are we going somewhere that my attire would be unacceptable? This is our private ship," she joked following him to the door.

"No your fine I guess." They walked out of the room with Teyla still in her pajamas headed to the control room.

***

"Hello," the AI greeted as John and Teyla entered the room.

"What's up?" John asked strolling over to the control chair.

"Teyla do you see the serum on the table?"

"Yes," she answered walking over to it and picking it up.

"It's a memory suppressant please inject yourself with it," he instructed and when she complied he turned too John, "In response to your question I was simply wondering if your plans had changed."

"Mine haven't, have yours Teyla?"

"No I will remain," she said adamantly.

"Good I'm glad to see you are going to continue."

"Is there any reason that we shouldn't continue?" Teyla asked taking a seat at a nearby console. She casually turned it on and perused through it using the knowledge of ancient she had acquired through the years of dealing with it.

"No, you can continue if you want." A few equations began scrolling across him, "I will be running some diagnostics."

"Well we'll just continue with what we were doing before I left and what we did yesterday," he said as he sat in the main control chair keeping an eye on Teyla. He pulled up a schematic of the ship and viewed the different rooms mentally checking off the rooms he had already been to. He eventually came to a room that he had not been to, he memorized the way their before moving over to another console where he began typing something on it after a few minutes Teyla walked over to him curious about what he could be doing.

"John what are you doing?"

"I'm just uh checking some life sign readings."

"For what?" she asked her interest piqued.

"Well I'm wondering what happened to you before you called me," he told her continuing to work on the console.

"Do not bother yourself with it any further," she asked but her eyes implored him to continue. "John but did you find anything?"

"No you were the only one there," he said stepping away from the console although he continued going through all the possible scenarios that could have resulted in whatever had happened to Teyla.

"Should we proceed to a new area of the ship now?" Teyla asked proceeding to the doorway.

"Ok let's go," he said reluctantly leaving the room as Ancient stared at him blankly.

***  
_Several Hours Later_

John was going through several pages of text when Teyla moved next to him her arm brushing against his, "John what does sweetheart mean?"

_Great she remembered just what I need Teyla realizing I have feelings for her_, "It's…It's a nickname for someone you uhh… someone you care for."

"Oh," she said realizing why John had seemed uncomfortable around her all day.

"Why where did you hear it?"

Her eyes went wide, _did I misinterpret what John had meant or did I mistake what he said for something else? _She thought.

"_I can get the audio records for the bedroom if you would like Teyla,"_ she heard the AI say in her head for the first time causing her to jump off the platform.

"Teyla are you okay?" John said moving down and putting his arm around her shoulders.

"Yes John, Ancient simply spoke to me in my mind for the first time it was unnerving to say the least," she said blushing at her reaction to something that she should have expected.

"Yeah I know he did it to me to," he said as she shrugged off his arm much to his chagrin.

"What did he say?" John said heading over to his own console he turned it back on.

"Nothing of importance."

"Teyla come check this out please," he said looking at a certain piece of text.

"Yes John," she said stepping over by his console and looking at the text.

He pointed to the line he was referring to, "What does that look like it says to you?"

"It refers to," She said pausing as she read further down the screen. "This would then seem to indicate that this ships commander had something to do with the Asgard," she said continuing to study the screen.

"Yeah that's just it how can this ship be that old? This looks like the Asgard are a relatively new race and is informing them that they will play an important role in the future. The message also seems to discuss cloning as if the Asgard had not yet even begun to look into that kind of technology."

"This ship is very old then John," she observed finishing up with the text.

"Thanks Teyla," he said smiling at her as she stepped off the platform and moved towards her own console.

"Any time John," she said returning his smile and reactivating the console.

***

Eight Hours Later.

"Teyla do you want to grab something to eat?" he said looking over her shoulder at her screen.

"What kind of food does the ship have?" she asked Ancient.

"Whatever kind you want," it replied smiling at the pair.

"I'd like a something simple just a salad," Sheppard said turning to Teyla to see what she would request.

"John what is the food you frequently talk about?"

"I don't know popcorn, Ice cream, Pizza?"

"Yes Pizza do you think that would be possible Ancient?"

"Of course you will learn this ship has much to offer in time your food will be ready momentarily you might wish to head to the dining room in the meantime," Ancient said leaving the two with a map to the dining room.

***

"John do you think I will ever get to see your world?" Teyla asked as they neared the dining room.

"Of course Teyla," he said sliding his hand across the door sensor. A moment later the door slid open revealing a very different sight then what either of the two had been expecting. The room was dark barely lit by a light or two hanging from the ceiling. The table at the center of the room appeared to sit four however it was only set for two. Every aspect of the room was in complete contrast to the rest of the ship. Where it was dark the rest of the ship was more than amply lit the room lacked any kind of advanced technology that dotted the rest of the ship. They took seats and their food was teleported in a moment later to their surprise. John picked at his salad while watching Teyla thoroughly enjoy her pizza.

"Is something the matter?" Teyla asked John unnerved at how he was looking at her.

"No it's just interesting to watch you."

"Oh," Teyla said blushing and looking away from him.

he felt it himself smiling at her reaction_ she looks so cute when she's embarrassed like that_; he thought when he saw her cheeks go red.

"I don't think I've ever seen anyone enjoy a pizza as much as you are," he said still smiling absentmindedly at her. When they finished eating Teyla returned to her bedroom and John headed to the bridge to look through the sensor logs again.

***

"Colonel Sheppard how was your dinner?" Ancient asked as it appeared on a nearby.

"Fine," he grumbled continuing to look through the sensor logs to see if he could find out what happened to Teyla.

"What is troubling you?"

"You should know your reading my thoughts."

"Your mind is clouded and confusing I am unable to make out many details," he claimed, confusion marring his brow.

"Nothing is the matter that concerns you just a little unhappy that's all," Sheppard said moving over to the control chair in the center of the room and sitting down.

"About your situation with Teyla?"

"She won't tell me what is really bothering her," he said closing his eyes and wishing the AI away he just wanted to be alone with his thoughts.

"I could always activate the security cameras if watching her would put your mind at ease."

"There are cameras inside the bedroom?"

"A few in every room, yes."

"I'll be taking those out in the morning," he told Ancient as he opened one eye to see what he was doing."

"And tonight?"

Sheppard laughed at the AI's suggestion, "sometimes you know me to well."

"Is that a yes?"

"Yes," the AI said as it activated the cameras in the bedroom.

"Where do I watch them?"

"Here however now would not be an appropriate time for you to watch."

"Oh," Sheppard sat back down in the chair and got comfortable knowing it would be a long night. "You're not watching the video are you?"

A screen appeared with the video of her room she was laying in bed resting she looked like she was reading something but he couldn't tell what. After a few minutes she discarded it and drifted off to sleep. After a few minutes he saw her began tossing in her sleep as the minutes went by she moved more violently and erratically he could tell that she was having a particularly bad nightmare. She began screaming something that he couldn't make out and after a few minutes of that he had had enough and quickly proceeded down to the bedroom.

End Chapter 9

A/N Well after reading that I think I made John a bit too emotional. I'm going to attempt to tone that down in future chapters but I don't think he was too outwardly emotional to anyone except Ancient which is done on purpose as John knows lying to him is useless.


	10. Chapter 10

Chapter 10

Sheppard ran into the room to see that Teyla was still violently thrashing about, "Teyla, Teyla it's ok," he said grabbing her arms and holding them. She looked up at him for a few moments still unsure of where she was she blinked a few times clearing her vision.

"John?"

"You were having a nightmare," he said releasing her arms but still remaining close to her on the bed.

"Oh," she responded moving away from him slightly, "John how did you know that I was having a nightmare?"

_Uh-Oh how am I going to explain this_, "I was sorta watching you."

"You were what?" she asked anger infiltrating her normally very calm demeanor.

"I was worried about so I had the old man turn on the video cameras so I could make sure you were ok."

"For how long?" she asked her anger temporarily disappearing at his concern.

"I don't know thirty, forty minutes," he said weakly.

She retreated further away from John, "John were you watching as I changed?" she demanded anger reentering her voice with a vengeance.

"No, No I had Ancient make sure that you weren't doing anything like that."

She eyed him suspiciously still unsure if she should fully trust him. "John how do I know that that is true?"

"Ask him," he said moving further towards the door. She looked him up and down deciding if she could in fact trust him.

"Thank you for your concern," she said before laying back down. He walked over to the door and as he strolled out of it but before the door could close behind him he turned around and stood at the door.

"Teyla if you don't mind me asking what were you dreaming about."

"I do not wish to discuss it," she said without looking at him.

"Is the memory suppressant wearing off? Because you've never really told me what happened in that room either so if you wouldn't mind I can't even try to help you if you don't tell me what happened."

"John I do not want to talk about it," she repeated to him again annoyed at his persistence.

"Ok but talk to someone at least I don't think it's just going to go away and taking drugs every couple of hours isn't the answer," he said leaving and allowing the door to close this time. As he returned to the bridge he saw that the lights had been dimmed and the video camera link had disappeared he sat in the chair and continued to work until he fell asleep from pure exhaustion.

***

He felt the sunlight against his eyes causing them to flutter open for a second causing them to immediately shut. He moved over and reopened his eyes slowly this time. He managed to slide out of the chair and move out of the room slowly making his way towards the mess hall. When he finally got there he slumped down in one of the chairs and closed his eyes, ancient chairs certainly weren't the most comfortable of places to sleep. He put his head down on his arms and slowly drifted off to sleep.

***

"John?" Teyla asked as she walked into the mess hall. He didn't respond she approached his still form and saw that he was sleeping. She smiled to herself he looked, so peaceful as he slept not the man she saw burdened by the responsibility of command as he called it. She sat across from him and waited for Ancient to finish preparing her breakfast. While she waited she watched his slow rhythmic breathing and by the time her food appeared in front of her she unconsciously had matched her breathing to his. When she had finished eating, he finally began to stir. His eyes slowly flickered open again and were greeted with the sight of a warm smiling Teyla, "Good morning John."

He groaned slightly and looked her in the eye his head still in his arms, "to what do I owe this pleasure?"

She continued to smile at him, "You do not look like you slept well," she accused lightheartedly ignoring his question.

"I didn't, those ancient control chairs aren't exactly comfortable."

"They do not look like they would be."

He raised his head slowly and began running his hand through his hair, "what time is it?"

"One in the afternoon," she told him as he blinked a few times clearing his vision.

"And I'm still tired; I really need to get a goodnight sleep I feel like I haven't had one in a month."

"Perhaps you should sleep in the bed tonight?"

"Where would you sleep then in the chair? Because I don't think there are many other places."

"I think the bed is large enough that we could share it," she said nervously she had not thought about where she would sleep.

John was stunned by her proposal it was quite tempting on the one hand nothing would please him more then to share a bed with the women he loved but she wasn't his she didn't feel the same way towards him. "I don't think that would be a great idea," he said smiling weakly at her. She returned his smile but both quickly directed their eyes away from each other. They sat that way for a few minutes.

"So where do you intend to sleep?" she asked interrupting their silence.

"I don't know… so where do you want to go today?" he asked desperately hoping she would allow him to change the subject to something he was more comfortable with.

"I found a small little room that I'd like to check out actually, but I don't know what you want to do."

"Ok sounds good, Ancient can I have some coffee please?" he said looking at Teyla while he waited for the coffee to appear a moment later it did, "Shall we?" he picked up his coffee and began sluggishly moving toward the door waiting for the coffee to kick in. Teyla got up and followed him to the door where she took the lead and led him to the small room.

***

"You know when you said a _small_ room I thought you meant a room not a closet," he said gesturing to the incredibly small room which looked large enough to fit only about three people at the most.

"I told you that you do not need to come with me John," she told him as she stepped up to the computer screen. As John walked around the room looking disdainfully upon the bland walls after walking around the room a few times he returned to Teyla's side and began looking over her shoulder.

"So what is this room for?"

"I believe that someone used this room to keep tabs on the populations of several worlds."

"Which ones?"

"Athos," she said stepping away from the console.

John immediately took her place and began reading, "there's a lot about you guys in here, you recognize any of this?"

"No this ship appears to have visited Athos many years ago."

John continued reading as Teyla moved towards the door, "Teyla."

"Yes John," she said stopping for a minute.

"Listen to this, a group of explorers arrived on the planet and the second in command appears to get along well with the Athosian leader. Teyla does that sound like us?"

"Yes John but that would mean this ship was near Athos a few years ago you said it was on that planet for 10,000 years."

"Ancient before we stumbled upon this ship how long was it on that planet for?"

"A little over 10,000 years," Its quiet voice said through the ships speakers although strangely he did not appear.

"Does this entry pertain to me and Teyla?"

"I am sorry but the nature of those entries is classified."

"And I was just starting to think he forgot we don't have clearance," anger seeping into his voice at being stonewalled again just as he thought that he was starting to make progress.

"I am confident we will learn the answers soon John," Teyla told him putting her hand on his arm in an effort to calm him.

"Yes I'm sure we will Teyla do you wish to continue?"

"Yes but you do not have to stay."

"Trying to get rid of me are you?"

"You still look tired and do not seem particular interested in this research."

"No, no it got interesting now that I'm in the story it's getting interesting."

They continued working for several hours when John decided to take a break and headed to the control room leaving Teyla alone in the room.

***

John strolled onto the bridge of the ship and sat down on the control chair activating it and bringing up several systems. He began attempting to activate different ones again generally some of the smaller ones that they were actually able to activate now such as internal sensors and the lights. Oh a whim he decided to once again try long range sensors and see if they would now respond to him. When he thought about bringing them online however he felt a strange sensation it was unlike ancient technology which felt like lifeless and mechanical, this felt warm and inviting like it had been waiting for him to turn it on. It encircled his mind and penetrated it completely implanting itself deep within his subconscious allowing him to control it without thinking about it. The sensors activated displaying a real time map of the system a few dozen ships were orbiting around in the same he looked more closely at one and an information tag appeared displaying the ships name, origin, builder species, class, age, weapons, and life signs, and classification. He saw a hyperspace window appear near the planet and a ship exited when it exited it was tagged as AES-HC6 immediately as more information quickly scrolled across the small tag. The ship contained a slight blue tint. A few minutes earlier Teyla had taken a break and headed up to the command center and walked up next to John unnoticed.

"What are we looking at?" She asked him as she studied the screen.

He jumped back at hearing her voice and turned to face her amused expression, "I got the long range sensors online its cool watching new ships come out of hyperspace. I wonder if you can you control the sensors?"

She looked at the screen for a minute concentrating, "No John I am unable to exert any control over the system."

As if on cue Ancient appeared nearby, "She will be able to control them with time just relax and let it come to you," They both nodded and turned their attention back to the screen. John expanded the sensors and detected other ships in nearby space he noticed that most of them contained a tint of yellow. Deciding that he should inform Atlantis about what they had just discovered a fleet of ancient ships and so very close to Atlantis only a few light-years. He sent a message off to Atlantis informing them of what they had discovered. A few minutes later they noticed a puddle jumper heading into one of the larger ships marked AES-CA1. They saw the ship disappear into a hyperspace window a few minutes later.

***

When AES-CA1 emerged from hyperspace half an hour later at its destination John and Teyla were still on the bridge attempting, unsuccessfully, to see if they could activate any other systems.

"John the ship has emerged from hyperspace."

"Ok let's see what happens," John said sitting in the control chair and focusing the sensors on that area of space. They watched as the puddle jumper exited the ship and headed towards the ships the jumper seemed to fly around several of the ancient ships but did not enter into any of them eventually after bypassing most of the ancient fleet they came to a final ship into which they entered.

A/N AES stands for Atlantis Expedition ship and refers to ships that the Atlantis expedition is using. CA stands for carrier and the one is the ships number and HC is Heavy Cruiser.

End Chapter 10


	11. Chapter 11

Start Chapter 11

A/N-Yes, this is a semi-regular update. I've got next week off to so I should be able to get some more work done.

The Jumper landed on the only ship that looked remotely space worthy, the others looked like they had been used as target practice for a few years. Several of the ships had broken and drifted apart making the journey across the fleet quite treacherous. The puddle jumper docked with the ship and the crew proceeded to enter into it and begin the lengthy process of clearing it. As the team slowly made their way towards the bridge of the ship none of the ancient systems sprang to life as the usually did. The team proceeded further into the ship they came upon the decomposed remains of the former crew not an unknown sight to those who had been on some of the previous recovery missions but still not a welcome one.

The team arrived on the bridge to fine a new and vile sight the bridge was covered in blood the Ancient control chair did not contain any hint of its natural colors and no one relished the job of cleaning out this bridge. Deciding that the bridge was a lost cause the team headed down to the Auxiliary control room. When the team arrived they saw that this room appeared to be sealed and several bodies lay just outside the control room with their blood stains against the wall they appeared like the people were attempting to get inside the Auxiliary control room. As they attempted to open the control room they found that the doors were locked. The team was unable to bypass the door control, so deciding that the only remaining option was to blast them open. After the explosion the team entered the control room and secured it. They saw that the room was in much better shape than the other one. Several bodies were strewn around the room haphazardly but there were no traces of blood in this room.

***

The team had managed to activate several ancient systems however most were nonresponsive they had been unable to activate weapons, internal sensors, and long range sensors. As the team continued to work some noticed that there were some strange sounds however upon investigation they were unable to find the source of the sounds however their inability to activate internal sensors did nothing to calm the nerves of the skittish scientists.

"Doctor are the hyper-space engines online yet?" Major Boyd asked the lead scientists after another scientist had asked his team to check out a strange sound.

"Not yet we almost have sub-light engines online though."

"That doesn't really help us with getting back to Atlantis," He told Dr. Dyer before leaving to search the ship again. The scientist returned to work attempting to fix the hyper-drive. As the scientists worked diligently to get the hyper-drive back online they continued to hear the strange sounds and send the soldiers on wild goose chases.

***

"Doctor this is getting to be a bit ridiculous every five minutes one of your scientists is reporting some weird sound." Major Boyd said angrily as he entered the auxiliary control room after returning from another search for strange sounds.

"Look I'm sorry but the bridge and doors have made everyone a little skittish."

"Well I'm giving my men a break so you can tell your scientists to stop reporting this stuff."

"Ok I'll tell them but I don't think that will help."

"Why isn't the hyper-drive back online you've had 6 hours."

"We don't really know it's almost like someone did everything they could to get the hyper-drive offline I'd say were looking at a few days work at least."

"Should we stay or can you bear to spend the night here?"

"We'll be fine don't worry."

***

_Aboard Ancient_

"John why has your team not yet left the ship?"

"I guess there having some trouble getting the ship back online," he said focusing back on the sensor screen.

"Why would they attempt to get the ship back online?"

"So that we can salvage it and send it back to Atlantis they're probably trying to get the hyper-drive online."

"Are you people insane?" Ancient said as he brought the ships engines online.

"What are you talking about?"

"You sent a team to repair a level 5 biohazard ship," he scolded.

John shot him a look, "what does that mean?"

"It means that there is a hostile, intelligent, adaptive species onboard that vessel."

"So we clear it out and then fix it."

"You cannot clear out this species it will kill your team the minute the hyper-drive is fixed," Ancient turned the engines on to maximum and headed for the upper atmosphere. After a few seconds it cleared the planet's atmosphere and entered hyper-space.

***

"Wait what are you going to do?"

"Destroy the ship."

"What about the team if the hyper-drive isn't online didn't you say they'd still be alive?"

"Yes if you wish you can try to talk to them but that ship must be destroyed."

"Ok let me send them a message."

"John what is happening?" Teyla asked as she entered the bridge.

"That ship we told Atlantis about is infected with some sort of hostile species."

"Is the team still alive?"

"Yes."

"For the moment they will not live long," Ancient added as the ship exited hyperspace.

***

Onboard the Ancient Ship

"Doctor how is the hyper-drive coming along?" Major Boyd asked entering the engine room.

"Well we should have it operational in a few hours with the help were now getting."

"That's good news is I'll tell the carrier they can head back to Atlantis now," Major Boyd said heading up to the command center.

***

"Colonel Sheppard I estimate that the hyper-drive will be online within the hour and your teams survivability rate against the infection in open combat is approximately six hundred to one."

"Ok send them a message telling them to get off that ship ASAP. And what kind of infection is it?" John asked as he moved over to a nearby communications console and began typing a message to send to the team.

"The creature you encountered years ago that Jinto released, this one is an ancestor of it. It still has a physical body, but it projects that dark cloud to feed off of energy as a hunting mechanism. The physical body does require sustenance.."

"It will feed off of the hyper-drive in order to grow," Teyla said moving away from the console she was working on over to where John and Ancient were located.

"Yes that would be likely although it would prefer to have access to a planet if it cannot access the controls it will feed off of the hyper-drive and it should be able to grow quite large and it will consume your team as well."

"Ok I sent the message we should see them either respond or leave the ship shortly."

***

"Major we've just received a message."

"From the carrier?"

"No sir it's from Colonel Sheppard," The technician said rereading the order confirmation in order to make sure that they were authentic.

"What really? The Colonel left the ship already?"

"I don't know sir."

"Ok what does the message say?"

"Classified, I'm sending it over to that console," he said indicating the one on the far side of the room.

"Thanks and send off that message to the carrier."

"Yes sir," the Technician said turning back to his work while the Major moved over to the console.

The technician turned, "Ok Major…" he stopped midsentence when he saw that the Major's face had gone completely pale.

"Order everyone to the jumper," the Major said distantly still staring at the message unable to fully believe its contents.

"Sir?"

"Just do it I don't have time to explain."

"Do I go there to?"

"Yes of course send it off and head there on the double."

"Where are you going sir?"

"The Main bridge."

"Why?"

"I have to activate the self-destruct."

"Why?"

"No time." Boyd made for the door, flipping the safety off, "MOVE IT CORPORAL!" the Major said as he left for the bridge in order to ensure that the ship was destroyed.

***

_Ancient_

"Colonel I see one life sign heading for the bridge of the ship."

"That's probably the Major he's probably going to activate the self-destruct."

"That would be unwise as soon as they realize what the Major is attempting to do it will kill him and anyone else on the ship."

"Can we contact the Major on the radio?" Teyla asked.

"Not without alerting the creature," number began scrolling across Ancient at a furious pace.

"Could you contact his mind?"

"No I could only do that if he was onboard the ship," The numbers slowed and began a more leisurely pace across him.

"What about another message would they not see that as well?"

"No one is in the room to receive it."

"What was your plan regarding the ship you didn't seem to think that the team had a shot of getting off I assume you were going to destroy it somehow correct?"

"Yes."

"How?"

"I am not unarmed."

"Ok now how powerful are the weapons you were going to use?"

"They would break the atomic bonds that make up the ship and all things contained within the ship," Ancient explained blandly as if he had done this thousands of times before.

Sheppard did a double take as he realized the amount of energy that would require, "wow that requires a bit of energy."

"Quite," he said annoyed at Sheppard's underestimation of his power.

"Do you have anything smaller like a missile?"

"I have less powerful weapons why?"

"Well if we open fire on the ship with those the Major might assume that the ship is going to be destroyed anyway and head to the jumper."

"Activating point defense weapon systems they should be ready to fire in a few seconds."

"That's quick can I see the ship and impact sites?"

"Yes," Ancient said bringing up an image of the impact sites and a damage report of the targeted ship on a nearby console. A few seconds later beams of energy cut into the ship burning away parts of the hull and activating dozens of alarms on the damage report screen. "He appears to have understood your message he is now moving towards the others. That is unfortunate."

"What?"

"It has awoken and is now moving to intercept your team."

"That's unfortunate? Those people are going to die do something."

"I can do nothing."

"Fire on ship target unoccupied areas away from the team it should move to the energy source," Teyla ordered as she watched the creature moving closer to the jumper.

"That will be insufficient."

"Just do it," Teyla again ordered and a moment later more weapons cut into the ship's hull vaporizing several decks and heavily damaging dozens of others.

"It is still closing on both the Major and the jumper."

"Keep firing just maintain a route for the Major and make sure the ship doesn't blow up."

"Understood," he said as a continuous barrage of energy weapons cut into the ship's hull.

"Is it working?" they both asked earnestly.

"It is now closing at a much faster pace although it appears to have split and part is now heading towards the weapons fire."

"So they have a chance?"

"A slim one."

"I'll take it now move your ass Boyd."

"It is unlikely that he will make it he is still several compartments away and the creatures are closing at a much faster rate now that it knows time is short."

"Take out part of the ship that is directly opposite the jumper that should distract them for a few seconds."

Ancient grumbled but complied and soon half of the remaining ship was vaporized and the damage reports seemed to indicate that the rest of the ship was falling apart with the atmosphere leaking out of most of the remaining compartments despite damage control measures. The remaining parts of the ship glowed an eerie orange as they boiled away under the intense heat of the energy weapons. "Your Major appears to be approaching the airlock."  
"Nice job now just get out of there."

"Uh-oh," Ancient said as he sent another salvo towards the ship impacting near the engine core.

"What?" John and Teyla asked looking at the screen for a clue.

***

"MAJOR LETS GO," the marine said firing his P90 at the monster.

"WHAT THE HELL IS THIS THING?" another asked no one in particular.

`"DOES IT MATTER IT'S UGLY AND IT SURE AS HELL ISN'T ON OUR SIDE," the Major answered as he ran towards the airlock turning and firing as he went.

"WE LOSE ANYONE?"

"A FEW, KAIDAN AND TWO SCIENTISTS DON'T KNOW WHICH ONES THOUGH," another marine yelled as the Major joined their defensive formation. They opened a salvo on the creature as it moved around the corner, the bullets caused it to temporarily retreat.

"IS THE JUMPER ONLINE?"

"YES."

"THEN WHAT ARE WE DOING HERE LET'S MOVE," he barked motioning for them to fall back inside the Jumper. They followed him into the jumper as the creature moved in on them taking one of the marines with them before they managed to close the airlock. When the airlock closed they all let out a breath before they heard the creatures attempting to break down the door. "Let's get out of here," Major Boyd said making his way towards the front of the jumper through the surviving members of the eight man team.

End Chapter 11

A/N-Reviews are appreciated and have a happy valentines!


	12. Chapter 12

Start Chapter 12

***

"I'm sorry but only five of the team survived," Ancient told John and Teyla.

John barely restrained from slamming his fist down. "At least some of them survived," Teyla said when she saw that John appeared quite angry at the loss of the soldiers and scientists.

"Three Teyla, three good men and women died on that ship that I sent them to," John said as he angrily paced around the room.

"John it is not your fault you could not have known about the creature."

"No I could have asked what the yellow meant and then I never would have told them about the ship and the team wouldn't have gotten massacred by that thing."

"Colonel Sheppard the ship has been destroyed and the survivors are heading towards the carrier."

"Take us home then," he said leaving the bridge.

"Go, he may need someone to talk to," Ancient told Teyla as she watched the doorway John had just disappeared through.

"I believe he will want to be alone now," Teyla said still staring out the door still.

"Trust me he wants to talk to you."

"I do not think so, apart from here on the ship we have not spoken much since I told him I was pregnant." She said turning and facing Ancient.

"Really? He speaks very highly of you and often said you two were quite close."

"Are you sure?" She asked surprised to learn that John didn't seem to be so angry it was much more in line with how he was now acting.

"Yes quite sure he has problems with his emotions something you are aware of."

She bowed her head in quiet submission, "I will speak with him," her voice barely above a whisper. She turned and left the room and making her way to where she thought John was.

***

"John what are you doing?" Teyla asked as she entered the dim room with the only illumination coming from the laptop John was working on.

"Letters," he said quietly hovering over the computer typing.

"I am sorry I interrupted," she said slowly retreating towards the door.

"No stay I don't mind," he said without looking at her as his hands dropped to his sides.

"John it is not your fault you could not have known."

"I told them to go get that ship I didn't ask what the colors meant," he said as he turned around to face Teyla.

"No one did that when the sensor array was found."

"But there was no one to ask when I activated that I could have asked the old man."

"John how could you have known? There was nothing to indicate the ancients ever transported anything like that on the ship."

"That doesn't change the fact that those people are dead and I sent them to that ship for no reason but I wanted to prove that this ship is worth it."

"This ship is worth it John we know so very little about it we just learned that it knew you when you came to Athos it knew you were there."

"But it won't tell us who even made him."

"He may tell us one day."

"But will it be worth those lives three dead."

"John do not blame yourself," She paused for a moment unsure if she should continue down her course, "come with me you can write the letters later."

He looked up at her his eyes desolate, "Where?"

"I have something I wish to show you," she said leaving the room with John in tow.

***

"This is what I wanted to show you," She said as they entered an observation room with a large glass dome overhead and transparent walls. She walked towards the window, "It's beautiful isn't it?"

His gaze wandered down from the thousands of stars down to her, "Yes the most beautiful thing I have ever seen."

She turned around, "When I was a child and I looked to the stars I was afraid, the sky was where the Wraith came from but now I see the beauty my father talked about when he would stare at them." She walked towards him their eyes met and held each other in an intense gaze, "That is because of you John you and your people have brought hope to this galaxy you come from far away on a world that has never known the Wraith and yet you fight and die for strangers, people who would turn their weapons on you when they meet you. Yet despite the hostility you encounter you fight on in order to free them from the Wraith why?" she said as she stopped in front of him, "because you feel it is the right thing to do and everyone on Atlantis feels the same way," She walked passed him, "otherwise I would not have stayed with you this long."

He turned around and faced her, "That doesn't change the fact that they died."

"No it doesn't but they understood what they were in for and they went on they didn't have to go to Atlantis but they knew the risks and felt it was worth it."

"I sent them to that ship," he said turning back to the stars.

"You did not know," she said walking beside him again, "Which one is Earth."

"I don't know, you know I can't believe you haven't been there yet."

"One day perhaps," she said as she headed towards the door leaving him alone with his thoughts again.

"Teyla…Thanks," he said turning to look at her before she left the room.

She smiled at him, "Your welcome John."

***

"Do you really believe that?" Ancient asked Teyla when she returned to the bridge.

"Yes they have conducted themselves honorably in my experience with one or two temporary lapses in judgment."

"And you do not think they fight the Wraith for their own selfish reasons?"

"They have their own reasons and their actions are not entirely selfless but they returned to this galaxy even though they did not have to."

"Yes I saw that they were forced from Atlantis for some time it was difficult on them Sheppard especially."

"Are you sure? From what I understand Doctor Weir took it the hardest."

"Perhaps on the outside. Sheppard, as they all were I'm sure, was very distraught at the thought of leaving you to behind to fight the Wraith by yourself."

"Well Ronon and I did not fight the Wraith while the Ancients were in control of Atlantis."

"You must have been happy to see him again?"

"I thought I never would have seen them again of course I was happy."

"Sheppard was especially overjoyed at seeing you were safe and willing to remain with him."

"Really?"

"Yes he missed you when he was on Earth did he not tell you?" Ancient said feigning ignorance.

"Well yes but not to the extent that you claim," she said calmly.

"Why did you take him to the observation room?" He asked as a few numbers quickly scrolled across him.

"I thought he might enjoy the view and I hoped he would understand that we are fighting for all those stars."

"Most of those stars do not actually have gates."

She smiled, "True." The door opened allowing John admittance into the room. Upon entering he gave them a weak smile before moving over to the chair and sitting down.

"Is there something you would like Colonel?" Ancient asked as he activated another hologram next to the chair.

"Take us back to Atlantis but otherwise no just want to get some sleep."

"Very well Colonel Sheppard although I thought you were going to be sleeping in the bed tonight I had hoped to run some simulations."

"Does being in the chair prevent you from doing that?"

"It would wake you so yes."

"What about the observation lounge?"

"You would not be able to sleep there it will be very loud," He said already knowing how the conversation would end having run the simulation several dozen times.

"Would it be ok Teyla? I'm sorry but I don't see any other choice," he said staring at Ancient.

"It will not be a problem John."

"Thank you," he said heading towards the comfortable bed and blissful sleep that he had so looked forward to during his first few weeks on the ship.

"What kind of simulations are you going to be running?" Teyla asked as she sat down in the chair.

"General diagnostics," he replied casually.

"That could not have waited until morning?"

Ancient dropped his smile and took on a more serious tone, "He needs the rest he won't get it in that chair or anywhere else on this ship for that matter I really hope you do not mind."

She thought for a moment it wasn't uncommon for her people to share a bed during difficult times and she had done so after her father had been taken. "I do not, however I think he is very uncomfortable with the idea."

"Yes he is but he needs to sleep and he will despite his discomfort at sleeping in the same bed as you."

"It is not common among them to share their beds with another who they are not intimate with," she said getting up from the chair and wandering around the room.

"Would you like me to activate the cameras in the room?" he said bringing them up without waiting for her response.

"What no I should not," she started before looking at the screen, "What the-- turn it OFF now." Ancient jumped back in surprise at her angry response.

"Why?" he asked as the video continued to stream in.

"This is not right I should not spy on him like this," She glared at the blue figure as the numbers momentarily paused.

"He watched you through these same cameras he told you did he not?"

"Not while I was naked I imagine that he would be quite upset if he discovered that I was watching him like this."

"You may be correct, I will reactivate the cameras when he is done."

"Thank you," Teyla said looking at the screens before they died.

"He is finished should I activate them again?" he asked and she nodded in response when the feed filled the screen again she saw him staring out the window. "This is more acceptable I assume?"

"Yes although I probably should not be doing this," she as he turned toward the camera smiled and shook his head. "Does it have sound it looked like he said something?"

"It does but I do not think that you should be listening in on him," he said as John slipped into the bed and closed his eyes.

"Why?"

"He may begin talking in his sleep and if he does he may not want you to hear what he is saying."

"Does he talk in his sleep?" She said concentrating on his mouth to see if it was moving at all.

"Sometimes, he may say something he doesn't want you to hear."

She nodded accepting his answer for the time being, "Why didn't you tell John about what the yellow meant?"

"I thought he knew and that he was sending a team to destroy the ship," he said regret written across his face.

"What was that thing doing on the ship?"

"I do not really know the Ancients may have been doing my research on ascension or perhaps they wanted to try and use it as a weapon by that time my part in the war was pretty much over that fleet was one of the last attacks before the siege of Atlantis."

"What happened to the fleet?"

"The Wraith attacked it perhaps that creature did help the Ancient ship although it appears to have turned on its masters."

"Why did they attack empty space there was nothing there for the wraith?"

"Now there isn't," he said turning away from her. The numbers slowly but continually slid across his figure.

"I don't understand…"

"The Wraith were starving for food they needed to keep fighting but all of their food sources were depleted so when they attacked a world the cullings were very violent they would take out entire worlds populations. In order to prevent the Wraith from doing so the Ancients would have attempted to relocate the people and used their fleet to buy the time. When they finished relocating the people they would take out the system in order to deny the Wraith the territory," he explained continuing to stare out the main window.

"Taken out?"

"Cause the local star or stars to go supernova and wipe out all life and planets in the system."

"That seems rather drastic."

"It was but that policy was implemented only at the very end of the war I think three star systems were destroyed due to that policy."

"Why was Atlantis not destroyed?"

"I'm sorry but that is classified."

"Haven't heard you say that in awhile."

"You can access the sensors now if you would like," he said turning back towards her.

"Can I listen into what John is saying?"

"No he would not want that," Ancient looked annoyed at having to continually repeat himself.

"Yet you allow me to watch him undress," she said a small hint of her previous anger finding its way into her voice but mixing with a little playfulness.

"I did not think he would mind that," he said causing Teyla to eye him suspiciously for a few minutes.

"I think I will retire now," she said still eying him.

"Goodnight Teyla."

***  
"I must go Teyla is approaching," Ancient said to the seemingly asleep Colonel on the bed.

"Why?"

"She did not know I was talking to you and I do not want her to know," he said disappearing.

"_Wait why didn't you tell her we were talking?"_

"_I have my own reasons and does this mean you are more open to using the mental link?"_

"_No," _Sheppard said curtly as he shut down the link and attempted to go to sleep.

***

The door slid open and she quietly made her way to the bed, "Turn off the lights please," she whispered. He complied a moment later turning the already dimmed lights completely off leaving only the light of the stars to illuminate there room.

End Chapter 12


	13. Chapter 13

Start Chapter 13

The sun filtered in through the window slowly waking Sheppard. In his first moments of consciousness John was greeted with the sight of Teyla sleeping peacefully in front of him. Unwilling to risk waking her he stayed there unmoving watching her rise and fall with each breath. When she finally began to wake she was greeted with the sight of a rising sun and someone else very close to her. "Good morning John."

"A very good morning," he said continuing to watch her.

"When did you wake up?"

"A few minutes before you," he said as the sun inched up making his eyes slightly uncomfortable.

"Why didn't you get up?"

"Didn't want to wake you and it's rather comfortable," he said sitting up.

"Well I'm up now."

"Uh-huh," he said falling back to the bed and closing his eyes hoping to get another precious few minutes of sleep.

"Sleep well?"

He murmured a response and continued attempting to fall asleep.

"Do you intend to get up?"

"No."

"Come on we have work to do," she said planting her feet on the floor and looking around for where she had put her clothes the previous night.

"You have work to do, I'm thinking of just staying here all day."

"Well I will be around if you need me," she said grabbing her clothes and walking out of the bedroom.

"So what were you saying last night Ancient?"

"How did you?"

"You're always listening I learned that a long time ago."

"I was wondering why you were so opposed to sharing a bed with Teyla."

"You really don't know?"

"I do not."

"Yeah right you're probably always reading my mind you know the exact reason probably better than I do."

"She is heading to the room she was in yesterday why?" he said changing the subject in order to avoid evoking Sheppard's anger again and his threats to remove Teyla from the ship.

"I guess she isn't done yet," he said as he himself got out of bed.

"Could you turn off your hologram? I'd at least like the illusion of privacy while I'm changing," Ancient complied with his order and shut off the hologram. When Sheppard was done changing he reactivated his hologram.

"Where are you going?"

"Find Teyla," he said walking out the door.

"Wait you just said you were staying in."

"Changed my mind."

***

"What's up?"

"I am reviewing the database for entries relating to my people."

"Find anything?"

"Yes quite a bit this ship appears to have been keeping tabs on us for some time along with several other planets. There are records here of our team on other planets."

"Really what missions?"

"The Genii home world, the planet where we discovered the Orion and several others."

"Very interesting find anything else?"

"Just information about my people."

"Like what?"

"Nothing that would interest you John."

"Come on try me," he said moving around the console to face her.

"Well currently I am looking at my father's time as leader it is very interesting some of these records are very detailed."

"So what did he do that you didn't know about?"

"He dealt with many worlds that I did not about also there were more cullings than I knew about. He also appears to have been bonded with another besides my mother."

"Is being married more than once unusual among your people?"

"Unfortunately no most remarry," she said pausing to make sure she had used the term—marriage--correctly, "after their pervious partner is taken by the wraith."

"So your father remarried?"

"Yes however he never mentioned his first partner."

"Is that strange?"

"For him I would think it strange he was very forthcoming about his life perhaps it hurt him too much to talk about it."

"You were never married were you?"

"Not yet although I hope to marry Kanaan when we find him," she smiled a bit at his memory.

"We'll find them Teyla don't worry," he said putting a hand on her shoulder. "Do you want to get something to eat?"

"I will accompany you to the commissary," she said powering down the console. They headed to the mess hall discussing what Teyla had learned that day.

***

"How did you sleep last night John?" Teyla asked after a lull in their conversation.

"Very good thank you for allowing me to sleep there last night," he replied sincerely.

"It is not a problem John."

"So what do you think we will be able to control next?"

"I do not know perhaps navigation or shields what do you think?"

"Well I'm hoping the engines and weapons but I'm thinking something simple like maybe some type of security system."

"Yes this ship's weapons would be rather effective if such a low powered weapon could damage the ancient ship like that," she said getting up and throwing out what remained of her own food.

"Are you able to use sensors yet?"

"I have not attempted to do so but Ancient said that I would be able to," she said sitting back down and taking a sip of tea.

"Why not you seemed anxious to use them before?"

"I was preoccupied at the time."

"With what?"

"I was watching you on the cameras," she said quietly blushing at her embarrassing actions but unwilling to lie to him.

"Oh really see I told you it wasn't so bad."

"Actually…" her voice trailed off and she started blushing again.

"What?"

"He opened the camera while you were."

He was beginning to become alarmed, "While I was what?"

"Naked," she said quietly.

John went livid; she contained a laugh as the color drained from his face. He decided to change the subject, "so have you asked about how Athos was monitored yet?"

She did laugh at his not so subtle change of subject, "Not yet however it is very strange and I think I am still missing something on those records."

"What?"

"Well they are eerily accurate about your time on there but is more vague about before you arrived for instance it merely mentions that Tagan, my father, was joined his partner taken and then rejoined with another but it mentions that we went to the cave together and that you picked up my long lost necklace."

"Yeah that's uh really weird," he said glancing around the ships walls with a perplexed look on his face.

"Are you able to use the sensors yet?"

"I believe so Ancient said I was able to but I have not attempted to do so yet."

"Why not?"

"I was preoccupied at the time for his behavior."

"Oh well why don't you try now?"

"Because I find reading the history of my people more interesting than playing with the external sensors."

"Ok well let me know when you're done I'll be playing around with the sensors and anything else ancient lets me do."

"Have fun."

"You to," John said leaving.

***

"Teyla told me what you did,"

"So she did."

"Did you think I wouldn't find out?"

"No, I knew you'd find out, but I do not think that you will do anything about it."

"And why is that?"

"Because I know you."

"Yeah more like because you know you can control my thoughts,"

"Do you really think I would do such a thing?"

"Yes and the scary part is that doesn't bother me. So my question is: are you preventing me from caring that your interfering in my mind?"

He smiled in response, "So you don't care if I interfere in your mind but you care that I might interfere in you caring that I interfere with your mind?"

Sheppard looked at him for a second before answering, "Yes but that does mean that you aren't completely controlling my thoughts."

"That it does," he said giving Sheppard a reassuring smile as Sheppard moved around and took a seat in the control chair.

"Can I control anything new?"

"Internal sensors but you have been able to control them for some time." Ancient responded and Sheppard activated them a moment later a virtual schematic appeared in his mind with a single dot representing Teyla still working in the room she had found the day before. He thought about activating the internal communications array and felt as if controlling it was just out of reach nearby but still out of reach. He got out of the chair disappointed that he had been unable to activate the system.

"Teyla are you busy?" he asked over the radio.

"Not really John why do you need something?"

"I'd just like to see you activate the sensors and see if you can do anything else," he said pacing around the control room calmly.

"Of course John I will be there in a few minutes just let me finish this," he could tell that she was slightly exasperated with him.

"Sure take your time."

***

"John sounds much better whatever you said to him as had a profound effect," Ancient told Teyla as she was finishing up with the page.

"Yes he sounds better now," she said continuing her translation.

"It is your doing so on behalf of both of us, I thank you."

"I believe that you also had something to do with it so thank you as well."

"My help was not as noticeable as yours." Teyla rolled her eyes at his downplaying of his own help.

"Well you still helped," she said powering down the console and opening the door in order to leave.

***

"Hey Teyla it is good to see you," John said merrily surprising Teyla with his amount of enthusiasm.

"Hello John," she greeted uneasily, unsure of what to do because he was sitting in the chair.

She stood their awkwardly for a moment before John sprang up out of the chair, "Come on I want to make sure it's not just me."

She approached the chair eying him suspiciously unsure of where his excitement was stemming from but she did not question him yet.

When she sat down she felt Ancients presence in all of the ships systems. She took a minute to take it all in as she had not spent too much time in the chair but after a minute she thought about long-range sensors and felt them approach her slowly encircling her mind after they mixed with her mind she understood how to use them. "John is this what you want?" she asked bringing up the sensors on the holographic display.

He smiled in response while excitedly pacing around the room again, "Yes that means that you don't need the Ancient gene to run this ship unless you need Ancient or Wraith genes to run this ship."

"John can you activate any other systems?"

"Internal sensors."

She thought about those for a minute and felt a similar feeling and then she found that she was able to control that system as well, "Good?"

"Thank you," he said still ignoring the strange look she was giving him.

"Is that all or?" she said getting up from the chair.

"No thank you although you're welcome to stay if you want," he said sitting down in the recently vacated chair.

"No I will return to my research," she said leaving the room.

***

"Ancient do you know why John was so happy," Teyla asked as soon as the door shut behind her sealing her in the room.

"Yes it is my fault."

Teyla stopped and Ancient read the confused look on her face easily.

"I needed him to be in a better mood so I put him in one," he said unashamedly.

"How?" she asked looking gently down upon his hologram.

"Do you really want to know?"

"I there a reason I wouldn't want to know?"

"I do not think you will like the answer."

"Then perhaps I should not know the answer but I have one question will you do the same to me?"

"No."

"Should I trust that you will keep your word?"

"You can there are many reasons why I could not interfere with you in the same way."

"That is all," she said to the disappearing hologram.

***

"So any chance of you telling me what is going on in this ship?" Sheppard asked jokingly.

"None," Ancient replied with a smile.

"Can you get me a beer? Sheppard asked as he moved over to the control chair wishing it had cup holders.

"I will have one synthesized immediately," he said and a few minutes later one appeared in Sheppard's hands. He took a sip before setting it down on the floor reluctantly. While in the chair he attempted to activate several other systems unsuccessfully.

"Is there anything new I can do?"

"Just the different features of the sensors and diagnostics," Ancient said brining up the internal sensor display however Sheppard dismissed it opting instead to run a diagnostic on the ships weapons systems. When the diagnostic finished it turned up nothing. Sheppard continued with the diagnostics of other systems he was unable to control and after some time he finally accepted Ancient's repeated requests for him to use the internal sensors.

"Let's see what else I can do with these since you won't let me use anything good," he said searching for the sensor with his mind attempting to look for alternative functions and other ways of using them. "Is this why you wanted me to use these?" he said as he activated the ships security cameras. He flipped through them quickly seeing all of the empty labs and then Teyla working in one of them. He found it strange to see so many empty rooms a few were dark but most were lit.

"Strange isn't it seeing so many desolate rooms?"

"What was it like for all those years with no one on this ship?"

"I was not active for most of those years but it is very strange how few people command this ship."

"Yeah I had a question about that why all these labs but only one bedroom?"

"This ship is not usually sent on long deployments so it has never really needed somewhere for a large crew to stay as they simply slept in Atlantis and the only person to sleep on this ship is generally the captain."

"That doesn't really seem to make a lot of sense to me but ok."

"You will understand it in time."

"Let's hope I have the time."

End Chapter 13


	14. Chapter 14

Start Chapter 14

"Teyla have you noticed any side effects?" Ancient asked as she arrived at her usual lab.

"To what are you referring to?" she asked sitting down on a nearby chair.

"Have you heard any of his thoughts felt any of his emotions or anything else like that?"

"I am not sure I believe I may have heard a few of his thoughts and I did feel his emotions regarding the men he lost.

"That is all?"

"Yes, his thoughts have become more frequent however they are for a short time and I do not think he has noticed."

"No, he hasn't but they will become more frequent and last for longer as you stay here."

"Is he hearing my thoughts as well?"

"Not yet I believe he is attempting to prevent that from happening."

"How can I do that?"

"You do not need to concern yourself with it you will grow accustomed to those thoughts soon enough."

"His thoughts and feelings are private I should not be hearing them."

"Has it not been a positive experience for you?"

"That is beside the point, if he wished to share his thoughts he would; I should not invade his privacy like that."

"I will leave you to continue your research." He disappeared quietly.

"Wait I have several questions," she said standing up and moving over to the console.

He flickered back to life, "What?"

"How is such recent data on this console about Athos me and John are on here that happened only a few years ago?"

"There are sensors around many worlds that transmit everything they gather back to this ship. Some worlds that you have visited contain those sensors but if you want that data than you will need to find those rooms."

"Why do you not translate these logs?"

"Because they are not mine to translate the ones that are have already been translated into English," she nodded and proceeded to go through the console learning more about her people.

***

"Colonel are you able to detect when Teyla is able to hear your thoughts?"

"No, why has that started happening already?"

"Yes several times in fact," he said cheerfully.

John groaned to himself, "What did she hear?"

"Your concern about calling her sweetheart, your thoughts about the men who died, and several others."

"Why haven't I heard any of her thoughts?"

"Because your mind was the first to enter into the system in time you will hear her thoughts,"

"Can you stop that?" he asked lazily.

"No, I cannot the system was not designed to be turned off."

"Ok well how soon will be hearing her thoughts?"

"I cannot be certain,"

"An estimate at the least," John was growing annoyed with the cheerful mood of the blue man.

"I do not know perhaps a few hours or even days."

Sheppard frowned at him, "Any new toys for me to play with?"

"The ships systems are not toys Colonel but you have control over the ships internal security system."

"Good," he said sitting down in the control chair and bringing up the security system. He looked through the different cameras at the dark labs and the hallways. He saw Teyla in one of the smallest labs, "I see you." he called over the internal communications system.

She turned around in surprise, she hadn't heard the door open, "John?" she asked seeing that the door was still closed and not seeing him.

"Yes," he responded playfully.

"Where are you?" she asked smiling and in her own playful tone.

"You don't know?"

"No," her response was deadpan, her expression told him that she was not amused by his game.

"Well maybe I don't want you to find me,"

"Perhaps I do."

He smiled, "I'm on the bridge I've got control of internal communications and security."

"Can you produce your own hologram?"

He turned to the AI.

"Yes I will activate them now,"

"Thank you," the image activated next to Teyla and she saw him smiling up at her.

"Interesting color John,"

"What color am I?"

"Pink," she said laughing slightly.

"What really?" he said laughing slightly, "Ancient any chance of changing my color?"

"No John leave it is entertaining to look at your little pink pistol," she said laughing.

"Oh is it now, Ancient come on something like a blue or green."

"Why do you continue to carry your pistol?" she said stifling her laugh.

"Because I don't want to be unarmed if something comes here and attacks us."

She turned back to her reading, "goodbye John."

"Don't you want to come up and try it out?"

"No, I have not finished with my people yet."

He deactivated the hologram and went back to exploring the security system.

***

After a few hours he had found weapons systems that could be used to defend the ship. He tested fire those and found them to be very effective although he had no real targets to attack. "So there's nothing for me to do with this stuff?"

"I can run some simulations."

"Fine," and no sooner had he said it then he felt the world fade and the simulation take its place. The simulation began by slowly sending troops against the ships formidable defenses but it steadily increased the amount and skill of his opponents. It continued to add variables such as someone who he had to protect; Sheppard noticed that person was usually Teyla. He managed to successfully defend against most of the waves of enemies which consisted of Wraiths, Asurans, and Genii. When the simulation ended he leaned back panting from the grueling hours of fighting. "_Wow and that was just simulated"_

"_Yes it can be very stressful controlling the drones but you seemed to do it with exceptional skill."_

"_I've had more practice than I'd like and the lasers were what killed me they took a few shots to kill the wraith so that got intense when anyone I needed to protect was around. The wraith just kept shrugging off the shots and getting to close."_

"_What did you think of the fields?"_

"_Well I wasn't very good with them because they are kind of strange to use but I can see they would be very effective."_

"_Yes it is strange to watch a Wraith get caught in a time dilation and see them get partially trapped their attempts to leave are often humorous." _

"_Why was it so exerting, I was just sitting here?"_

"_It simulates the stresses that would be exhibited in that combat situation by both the user and any soldiers defending the ship. It actually went easy on you." _

She walked into the room and saw him sitting in the chair sweating, "John what are you doing?" Teyla asked entering the room and interrupting their mental conversation.

"Oh Teyla I was just running some simulations they were realistic."

"It would appear so," She eyed his sweaty T-shirt.

He got up from the chair, "So what's up?"

"I simply wished to inform you that I am finished with that lab and am free to join you," she sounded cool to him and what she figured he'd have her doing.

"Would you like to try the simulations?"

"Are they dangerous?" her hand and eyes drawn to her belly which was beginning to show.

"No, well at least I don't think so."

"They are not harmful," Ancient said curtly without appearing.

Teyla looked at John who gave her a reassuring smile before stepping out of her way. She sat down in the chair and slowly searched the system for the simulations John had been using. When she located them she studied them for a few minutes before activating them.

***

Several hours later she sat up with a start looking around she noticed that John was sleeping nearby with the remains of his dinner and that it was now dark outside showing the hundreds of stars of the galaxy. She took the food John had left for her, which was now cold, and headed to the observation lounge. "Can you heat this up?" she asked Ancient on her way there.

"Yes but you will need to head to the dining area."

She changed course and headed to the mess hall after having her food heated she headed back to the lounge and sat at one of the tables. When she finished she moved over to one of the rooms' couches and laid down. She drifted off to sleep staring at them marveling at how something so beautiful was filled with something which had brought so much death to the people of Pegasus.

***

She walked into the building alone she had been separated from the rest of her team but she knew that they were scouring the area. She made her way through the buildings destroyed entrances into its relatively intact interior. As she made her way into the first room she noticed that technology in this building was different than that of the others. While the other buildings appeared to have 19th century technology this one definitely had some advanced technology. She activated her radio, "hey sir you might want to come here there's something you should see," she asked cheerfully on his channel.

"Oh really what might that be or should I say who?" he replied playfully over the comm. Channel ducking away from his teammates who were lurking around.

"No there's some technology here for you to check out although I'm sure that's not all you'll be checking out," she said suggestively smiling to herself.

"How well you know me," he said laughing to himself.

"You know talk like that could get you into trouble with the higher ups," she replied as she moved further into the building.

"Maybe but you're not military so I don't see what the problem is."

She laughed it had become a sort of ritual, to tease each other, between them since their friendship have first evolved. They'd hadn't told anyone about it yet and their team had only just begun going on missions again so they hadn't encountered any problems but they both knew that they would have to tell Carter sooner or later. "Just get over here," She turned around and slowly meandered back to the entrance.

"Alright relax I'm almost there," he began tackling the debris blocking the entrance and after a few minutes managed to get inside the building. He greeted her with a kiss when they caught up with each other. "Come on, I think it might actually be wraith technology." They moved further into the facility weapons raised prepared for the possibility of wraith contacts in the area that hadn't shown up on the Life signs detector. When they came to a large door they it open and when they entered the cavernous room were greeted by a gruesome sight. There were many bodies lying on some sort of machine they had died recently. As they slowly approached scanning the room to see if any threats remained. Unable to find any they approached the bodies who were lying only a few hours before and when they approached them she gasped her mouth dropping open.

"What?" he asked her.

"Those…That's… These are the missing Athosians." He looked at the bodies again seeing the resemblance to some of the faces he had seen around the around Athosian camp.

***

Teyla opened her eyes slowly and then quickly shut them again she pulled her blanket up closer in an attempt to keep in some of the warmth. After settling back down under the blanket with a contented smile on her face she realized that she hadn't fallen asleep with a blanket the previous night. Her eyes flew open and she bolted up looking around the room which she was surprised to discover wasn't the observation lounge but her bedroom. She looked around for John but he had already left, when she didn't know. She decided to try and get a few more hours of sleep before getting up so she turned over and closed her eyes again.

As she drifted off back to sleep she heard the sound of the door opening and someone entering. She lazily opened her eyes and saw John putting a tray of breakfast on the nightstand. He carefully set it down in order to avoid waking her as he turned to her he smiled before leaning over and pulling the blanket up under her chin. He turned and looked at something in the corner before moving over to the window and staring at the horizon. He nodded to the corner and palmed the window sensor turning it from transparent to opaque blocking out the sunlight and plunging the room into darkness. He walked out turning and stealing one last look at her when he reached the door.

He watched, as he always did through the cameras, as she drifted off back to sleep with a smile on her face. _Perhaps she does care for him in a similar way, which would present an intriguing scenario; I must remember to input those parameters into the training simulations. _

End Chapter 14

A/N It'll be explained in the next chapter don't worry.


	15. Chapter 15

Start Chapter 15

"Getting an IDC?" Colonel Carter asked as the incoming wormhole formed.

"Major Irving's team," the technician called lowering the shield without waiting for the order.

Carter walked over to the technician, "they're back early." As the team walked back early she was relieved to see that none of them appeared to be hurt. As the team entered the gate room she moved down the stairs to greet them and ascertain why they were early.

When he saw her walking down the stairs he looked over the scientist at his side and gave her a reassuring smile it was going to be a long debriefing. "I'm afraid we've got some bad news Colonel."

she had known that since he had first walked through the gate but his tone and concerned look to his teammate and told her that whatever it was it was worse than what she had excepted, "What Major?"

"We've found some of the Athosians," he said giving a sideways glance towards the scientist.

"They were dead," she said sheepishly.

"Are you sure?" Carter's mind was already attempting to deal with all of the ramifications this would cause.

Irving nodded to the rest of his team that they could go and get changed, "Yes we're sure I saw them myself you'll need to send someone to check it out and do a full autopsy of the bodies I don't know what killed them but they weren't exactly normal."

"What do you mean?"

"Can it wait for the debriefing in ten minutes?"

She nodded and headed to her office where she called Rodney and Ronon to the briefing room.

***

"What's up Sam?"

"We've found the Athosians,"

They heard it in her voice but asked anyway, "Dead?"

"Yes hopefully it's not all of them; Major Irving's team will be here in a minute for a full debriefing."

They both took a seat Rodney incessantly hounding Sam for answers she didn't have and Ronon just sitting there. After a few minutes the team arrived took their seats and began the debriefing.

"When we first arrived in the city it looked pretty deserted so we headed into the buildings searching for anything," the Major nodded to the scientist indicating that she should continue.

She took a sip of water nervously before continuing, "I entered what looked like some sort of hospital but when I got inside the technology was much more advanced than what they should have been there. The rest of the buildings looked to be early industrial revolution but the medical technology looked like it might have been wraith. When I got further into the structure it was obvious that it was wraith tech I was seeing and then I saw these well I guess they were some kind of pod,"

"By that point I was there and I saw the bodies to, it took me a minute to see that it was the Athosians but it was definitely them although they were different."

"Different how?"

"I don't know how to describe it just they were different like not completely human."

"What do you mean?"

"Their faces didn't look entirely human I mean they were human but different they weren't hurt but changed like some sort of mutation."

"Ok Rodney I want you to check it out see what the wraith were doing to them Major Lorne's team will be leaving shortly. Ronon I'd like you to talk to Teyla she'll probably want to come back and see who it is."

They nodded at least it was only four or five Athosians but that didn't tell them where the rest were; as the team got up and left they were solemn their closest allies who had been missing for months had just been found dead.

***

The pilot landed the jumper and lowered the exit ramp without saying a word, "Do you need me to stay or is Colonel Sheppard going to take you back?"

"You can head back," he said leaving and jogging towards the ship. When he entered he headed towards where he remembered the command center was. The ship was lighter then he remembered it had been dark and difficult to navigate it was now very brightly lit with blue and white lights as he approached a corner he heard two people talking one he knew was Sheppard but he didn't recognize the second one. They were speaking quickly and their sentences didn't entirely make sense they seemed to be speaking in half sentences as if they read each other's mind and only spoke some things out loud.

He rounded the corner, "Hello Ronon."

"Sheppard I need to talk to Teyla do you know where she is?"

Sheppard turned to the pedestal where the blue hologram resided, "Ancient where is she?"

"Sleeping in the bedroom,"

"Which bedroom?" Ronon asked Ancient nervously.

"There is only one Specialist Dex and I'm sure Sheppard will be happy to escort you there,"

"There's only one bed on the ship?" he asked with a raised eyebrow at Sheppard.

"Yes, I've been sleeping in the observation lounge."

"hmmp let's go,"

"So why do you need to talk to Teyla?"

"We found some of the Athosians," he said sadly.

"Are they ok?"

"No. They're dead," he tried to deadpan it, but John could hear the sadness in his voice.

"Shit that's not good."

"Was Kanaan among the dead?"

"I haven't seen the bodies sorry Sheppard," he said following Sheppard down a hallway towards the bedroom. As they approached the room Sheppard sought out Ancient with his mind and made sure that Teyla was still sleeping. When he saw that she was he opened the door and walked in quietly Ronon followed although he did not enter as quietly and as John sat on the bed and gently woke Teyla he raised an eyebrow at him.

"Teyla you have to wake up?"

"Why what did you turn on now," Teyla groaned sounding slightly bored.

"No Ronon is here he has some news," John sounded sad.

"What is it?"

***

The team entered the hospital however they were armed not with P90's this time, but with body bags. They quickly packed the bodies up before they started their work on the wraith equipment. Rodney ordered the other scientists about the facility while leaving the main and most important room to himself. Doctor Keller sent the bodies back to Atlantis back for a full autopsy while she remained behind where she assisted Rodney with the medical technology.

"Don't touch that," Rodney warned her however she ignored his warning and proceeded to peruse through the console she believed contained medical records.

"Rodney I need you to download this to a computer and bring it back to Atlantis," she said after reading the first few sentences.

He grumbled something but complied as she packed up the chemicals she had found in the lab. She had been able to collect several samples from around the lab along with some data from a wraith terminal. It wasn't the kind of work she was used to but she did it nonetheless. While she didn't relish her task she couldn't imagine how difficult Ronon's task would be. Rodney turned handing her a tablet "Anything else?"

"No, thank you Rodney," she said carrying the bag and heading out the door towards the gate.

End Chapter 15


	16. Chapter 16

Start Chapter 16

"That went better than I expected," John said walking out of the room leaving Teyla alone as per her request.

Ronon grunted walking along the hallway opening every door he came across "Is there a gym anywhere on this ship?"

"Yeah come on," a smile spreading across his face Ronon hated to be cooped up and knowing that the Athosians were in danger probably didn't make it any better.

***

Ronon was whopping Sheppard's ass worse than usual due to John's lack of practice. As Sheppard picked himself off the floor for the sixth time since they had started Ronon started to complain, "Man you really suck now, I would have thought you and Teyla would been sparring."

"Yeah well I guess she just didn't want to," he said striking out at the Satedan who easily blocked and countered. "We've actually found some cool stuff and I think being here has taken her mind off of missions for awhile."

"She must have not liked being away from the search for her people though," he said hitting John on the arm.

"Actually we found some information about her people so that kept her really busy apparently there's stuff about me in there to but I didn't look at it."

"Anything about any of us?"

"Teyla but I don't recall anything about you or Rodney I can show you if you want," he offered just dodging a vicious blow to his abdomen.

"Naw I'm fine," he deflected Sheppard's blows and started back with a few light one's of his own, "So what have you and Teyla been doing?"

"Mainly research and well you know about the ship you?"

He shrugged, "Usual missions sparring and Rodney got engaged to Katie Brown,"

"Really he finally proposed?"

"Yeah he got trapped with her in a room and Atlantis went into lockdown fortunately we were able to get some people down from the ships in orbit to rescue us."

"Where'd you get trapped?"

"Infirmary with Keller,"

"How was that?"

"eh she wanted to get to know me better."

"You two hook up?"

"No," a hint of sadness snuck into his eyes as he remembered the woman he had lost on Sateda.

John seized the momentary distraction in his sparring partner and managed to land a few blows, "Still too soon?"

Ronon recovered and sent a fury of blows at John forcing him back, the series of attacks was all the answer John needed as he once again fell to the floor. They shared a smile at how well they knew each other, and what the other needed. As John picked himself off the floor he indicated that he was done with sparring for now.

"What about you and Teyla?" he asked throwing his stuff back into the bag he had brought with him.

John picked himself off the floor leaving the rods on the side of the room, "What about us?" he warned causing Ronon to smile amusingly at him. John took the lead and headed to the nearest teleporter. "Where do you want to go?"

"I don't know its your ship what do you do here?"

He tapped a button on the screen, "Come on I'll show you the bridge that might interest you."

***

Sheppard sat down on the control chair as he walked into the room and looked to see if there was anything he could do to interest Ronon finding nothing he decided to look for Sateda in the ships database. "Hey Ronon check this out," he pointed to a screen off to the side that flickered to life and filled with text. He saw Ronon's confused look and got up from the chair, "it's about Sateda actually I don't know how it has this information but look here this about when the Wraith recaptured you and sent you back."

Ronon grunted but made no attempt to look at the data. "Not a fan of history I presume. How about hmmm," he thought for a moment.

Ancient interrupted his chain of thought, "Perhaps Specialist Dex would enjoy a battle simulation?"

"What kind?" Ronon asked Sheppard as he got up from the chair.

"Just get in Ronon," he said smiling and heading over to the door. He turned and looked at Ancient nodding to him as he left the room.

***

After 20 minutes of watching Ronon sitting in the chair John had left the bridge and headed back down to the bedroom. As the door slid open light filtered into the room he noticed how dark the room was for the early afternoon. He glanced around at the candles Teyla had laid out around the room he spotted her on the floor meditating, "Teyla?"

She had been meditating since they had left her so many hours before and had finally been starting to obtain some control over the emotions that had raged within her, hate, despair, anger, and hopelessness. But when he had interrupted he caused others to join the fray. When she had initially told him about her pregnancy he had been angry and avoided talking to her. But since arriving, he'd most definitely been kinder he'd been offering to help her and generally their friendship had begun to return to its previous state, a pleasant surprise for her after the weeks of little awkward contact. "Yes John?" She asked continuing with her meditation not even opening an eye to look at him.

He walked over to her softly and sat in the position he had been taught years ago by the now ascended Teer. He sat quietly for a few minutes waiting for her to finish. She bowed her head which he took as a sign she was finished however he still spoke in subdued tones, "When do you want me to fly you back to Atlantis?"

Her eyes flickered open gently and she faced him, "If you do not mind I would like to prepare before I see them."

He nodded, "You know that I'm…we're here for you and if you need anything we'll be happy to oblige."

"Thank you John I know."

"Then I guess I'll leave you," he started to stand up when she placed a hand on his knee.

"You may join me if you wish," she smiled warmly at him.

"Are you uh sure I'm not the greatest at mediating."

"Yes John I would…appreciate the company."

***

"Doctor?" the marine asked as he entered the room that had previously held the two Athosians. He was met by a series of turned heads and various forms of yes, "Doctor Keller," he corrected causing many to turn away grumbling.

"Yes Lieutenant," she asked from across the room head buried in the readouts on a tablet.

He approached her, "Colonel Carter would like to know when you're going to be ready to return to Atlantis she'd like a report on your progress here." He turned and walked back towards the door loitering just outside waiting for her to emerge. When she did he led the way towards the gate attempting to start a conversation with her but finding that she wasn't interested in any small talk.

"Doctor have you made any progress?"

"Yes, where is Rodney?"

"Probably in the mess hall, the briefing is in 20 minutes and you know him and food."

She nodded and headed to the mess hall.

End Chapter 16

A/N Read and review please, thanks.


	17. Chapter 17

Start Chapter 17

"Rodney?" Keller asked softly.

He mumbled something while continuing to finish of his lunch. "So did you find anything on the planet?"

She sat down next to him with a drink, "Yes did you happen to figure out whose lab it was?"

"Michaels he was doing research on," he started before taking another bite. "On his hybrids, he stopped early that's why they died. I guess he doesn't want his experiment discovered yet."

"Probably just waiting to stab us in the back again."

"Have you seen Teyla yet?"

"No but if she's not here already she should be arriving shortly why?"

"I just wanted to make sure she's ok I mean this is the first hint of her people in months and it's because they're dead."

"Well we could go check," Rodney said getting up and heading to the door.

She got up and followed him.

***

As Teyla finished her meditation she saw John sitting patiently on the floor behind her she smiled at him, "I am ready."

He nodded in response and stood up slowly quietly making his way over to the door nearly asleep from the meditation. "I'll tell Ronon," he said leaving and calling Ronon on the radio to apprise him of the situation.

Ancient appeared a deep blue just outside the door as it slid shut, "John you do not have to use the puddlejumper to get from here to Atlantis."

John looked at him incredulously, "how?"

"This ship is equipped with several teleporters that can transport you to Atlantis. I can instruct you in their use as soon as Ronon vacates the chair." John headed up to the bridge and pried Ronon out of the chair long for the AI to give him lessons on using the beaming technology.

***

John went down to see Teyla and help her bring some of her stuff up into the room as he was heading down he ran into her, "hey Teyla head to the lounge."

She looked at him confused as to why she would head there when the jumper was outside.

"Ancient is allowing me to teleport you guys to Atlantis it'll be much quicker."

"You are not joining us?"

"No I figured I'd stay here and take the jumper back"

"Why do you not teleport with us?"

"Can't, someone has to stay behind."

She raised an eyebrow at him, "And you do not wish to join me."

"No it's not that I just thought that..." his voice trailed off as he turned a looked out the window.

"That I would not welcome your presence?"

John's discomfort became evident to her without even looking at him. After a moment to collect his thoughts he answered still staring out the window at the forest, "It wouldn't matter Ronon can't fly the jumper he'd have no way of getting back."

She nodded and left him alone knowing that she wouldn't get anymore out of him.

***

Teyla emerged from her solitude with a bag on her shoulder and the rest of her stuff packed, the message was clear. She wasn't coming back. He headed down and they brought up the remaining bags and placed them and the lounge admiring the planets beautifully blue sky. "Ready?" John asked as he and Ronon entered the room.

She took a breath steadying herself, "Yes."

"Well I…I don't…" he paused for a minute, "Let us know if there is anything we can do."

"Thank you again, John," she said to his retreating back as he headed towards the control room to send her and Ronon to Atlantis.

"How has Atlantis been?"

"Sheppard didn't tell you?"

"Not entirely he told me that Rodney got engaged."

"Yeah they had a party and then went off to Earth for a week or two."

"Why were we not invited?"

"Rodney said he sent you guys a message but didn't get any response back."

Teyla stopped and turned to face Ronon, "What?"

"We sent a message but we never got a response."

"Excuse me Ronon I must speak with John before I leave." She left before giving him any time to respond.

***

"JOHN" she yelled after him as he turned the corner at the end of the long hallway she wasn't sure if he hadn't heard her of had ignored her but she followed him nonetheless. As she rounded the corner she began running in order to catch up to him, "JOHN," she called again this time he turned around and jogged back to meet her.

"Teyla what's wrong?"

"Ronon told me that we were invited to a celebration back on Atlantis but you never told me of it."

"I never got the message in the first place," he was initially confused at her anger considering even if he had hidden it, it would be a rather minor thing. Then it dawned on him, she wasn't angry about some party she was just looking for an excuse to get angry.

"You truly did not know?" She seemed to realize how irrational her anger was, but her voice still contained a slight edge.

"No what you thought I hid it from you?"

"I was unsure if you would have been willing to take me back and forth and considering you are remaining here as opposed to coming to Atlantis…"

"Teyla I told you Ronon has no way of getting back he can't fly a jumper I can and this way you'll get back faster."

"And why can Ancient not simply transport us?"

"Well I suppose he could but I…I don't want to uh leave the Jumper," he said looking at the floor knowing it was a weak excuse but he didn't think he could handle seeing Teyla and her people it was bad enough for him to see the pain she was in from hearing about it but seeing them and preparing for their ring ceremonies. She nodded accepting his decision and left him alone.

***

Their radios crackled to life in unison, "ready?" Sheppard asked.

Ronon replied for both of them, "Yes."

Sheppard powered up the old teleportation system and activated it sending them to the top of Atlantis's main tower. After their arrival Sheppard tracked their progress using the ships life signs detector.

***

They made their way down the central spire and when they reached a transporter Teyla headed to her quarters while Ronon headed to the control room to inform Carter of their return.

A/N-Read and review please. I'm sorry for any spellings/grammar mistakes, but I'm trying to close up my Atlantis stories starting with this one, so I'm putting a bit of a rush on it.


	18. Chapter 18

A/N-Soon enough dispatcher?

Start Chapter 18

"Where is she?" Carter asked Ronon and Keller when they entered her office.

"I don't know she left after seeing them."

Carter nodded in understanding there was no way to prepare yourself to see someone that important to you.

"I don't think that she was ready to see it, she didn't say anything."

"But she'd want to be strong for them," Ronon added taking a seat.

"Ok when you see her tell her that we're here for her if she needs anything at all," Carter stood up and walked over to the window looking at the gate.

"She knows."

"What do we do with the bodies?" Carter watched as the gate opened and the team she had been expecting walked through. She returned to her seat, "When the Athosians had other deaths they had a village but with just Teyla…"

"We could send the bodies back to Earth, but I don't know what Teyla will want to do." Keller stood up and looked at the gate herself, "Is that my team?"

"Yes I'm sorry we couldn't stay any longer but there are other Ancient ruins we need to research."

"Has Sheppard arrived yet?" Ronon asked as Keller retook continued to watch her team filter into the room.

"No why was he supposed to be coming soon?"

"Yeah he was supposed to be bringing the jumper back," Ronon said standing and moving towards the door.

"I can't believe he's abandoning Teyla, she once told me he said you guys were family," Keller said taking her seat again as the gate shut down.

Ronon stayed inside for another minute knowing why Sheppard really hadn't joined them yet but he didn't voice his opinion. "I'm going for a run." As he turned to leave he bumped into Major Lorne who was just entering the office.

"Colonel, Doctor," he greeted as Ronon quickly left the small office.

"Good Major we were discussing Colonel Sheppard's absence."

"Yes I wanted to talk to you about that as well," he took a seat in front of her.

"What about it?"

"I wondered if we could grant Sheppard permission to land the ship on Atlantis."

"I was considering as much it doesn't appear that the ship has any malicious intentions towards us."

"Was that all?"

"That and the team from Michael's planet just returned."

"Thank you Major, oh and send a message to Sheppard telling him to land the ship here."

He nodded on his way out.

"Was there something else you wished to discuss?" Carter asked seeing that Keller was making no move to leave her office.

"Yes I was wondering if I could lead another team to the planet in a few hours."

"Short or long term?" Carter tapped a few buttons on her tablet moving some duty schedules around.

"Short, there are just a few more things I'd like to do," she said getting up and heading towards the door.

***

"John you have received a message from Atlantis," his voice drifted into the virtual world John was inhabiting.

"Show it to me," he said continuing to explore the different systems slightly annoyed at the interruption. When it appeared however and he read it his annoyance at the interruption was quickly forgotten. "Hey you know how we talked about letting me fly and maybe use some of the weapons systems."

"Yes John," he responded appearing full sized in the virtual interface clearly not amused by John's pending question.

"Well I think perhaps you should finally let me fly this thing."

"They have finally given me clearance to land on Atlantis again?" he asked although still disinterested in the turn of events.

"Yeah I'm sure a few of the scientists are going to try and tie your power supply into Atlantis in order to save some of the ZPMs energy.

"Atlantis has a ZPM?" Ancient now appeared very interested in this new information and John felt the ships engines firing up.

"Yeah you didn't know?"

"I did not this is interesting."

"Yeah so can I fly this thing?"

"Yes John try not to crash it."

"Yeah I'll try," he remarked as he felt the ships engines begin to respond to him. It was similar to that of a jumper and although the ship was much larger it handled better he had no doubt that this thing would be good in a battle. The ship felt good to fly it was something it hadn't done in a very long time and it flew beautifully. The on board AI made all the minute corrections and augmented John's own flying skill with his ability to immediately act on what instructions he was given by applying the appropriate amount of thrust something which would take a human some time to calculate and even then there was some degree of error. While the flight was short John took the long way around the planet and did his best to put the ship through its paces. The two worked as a perfect team as the thought just began to form in John's mind Ancient converted it and acted upon it immediately while he regretted the reason he was able to do this, it stemmed from years of continuous combat and was necessary for his survival, he knew that for someone such as John having such a responsive ship would be a joy to fly. "Open a channel to Atlantis," he ordered and a click a moment later confirmed that it was open.

"Atlantis we are overhead where do you want us to land?"

"Colonel that was rather quick and same place as the Daedalus lands."

"Yeah this thing is a dream to fly I'll be down momentarily."

As the ship slowly descended through the clouds John was totally absorbed in making sure the landing went perfectly but such a routine action did nothing to distract Ancient. While John had access to the ships numerous sensors and was making use of most of them he failed to notice the solitary figure on one of the tallest, most secluded balconies.

She watched as the ship broke through the clouds almost directly above her the ship flew right in front of her startling her and causing her to forget her grief for a moment as the ship itself seemed to be smiling. She knew what it meant there was only one who would possibly be allowed to drive it. Armed with this knowledge she made her way inside and to the nearest teleporter.

***

As he stepped off the ramp for the first time in months the downpour started. He saw his friends who had been waiting for him head inside to wait for him but he was in no rush to head back inside. He had been inside the ship for so long that breathing fresh air and feeling rain on his skin that he longed to remain in it for just a few more minutes. As he stood there eyes closed enjoying the weather he failed to notice the door open or one of his friends approach him. She stood in front of him enjoying the rain herself. "John?" her voice belayed the true pain she was in and while she tried to be strong for everyone she needed someone to tell her it was ok in the past it had been her father then Charin followed by Doctor Heightmeyer and now she sought such support from John.

He opened his eyes slowly looking at her, "hey you're going to be ok," he told her as he enveloped her in a hug. He knew she was crying silently when he felt her warm tears on his chest a sharp contrast to the cold water falling around them, "hey it's going to be ok we'll find them ok?"

She stayed there for a few more minutes before the cold rain caused them to retreat inside where there remaining friends waited to greet John. As they began their hellos Teyla retreated out of the room and into another teleporter escaping everyone once again for her own thoughts and solitude.

***

After enjoying a nice lunch with Rodney and John who had joined her about halfway through Carter was returning to her office when she heard the gate activating. Knowing that only a few teams were off-world and none were due back for at least a day she hurried over to the technician. The gate activated and a moment later the code came through immediately and was a distress code from Keller's team. Carter called for medical and security teams to report to the gate room immediately. She was relieved when the first person to walk through the gate was unharmed followed quickly by several other unharmed personal. As Keller stepped through the gate she ran up the stairs calling for Carter to call several key personnel into a meeting.

End Chapter 18

A/N-Reviews are always appreciated.


	19. Chapter 19

A/N-It's short, and I probably should have combined it with the next chapter but I wanted to get it up quickly.

Start Chapter 19

"What happened?" John asked taking a seat.

"As soon as we stepped through the gate we saw a dart heading for it," Keller explained looking at the rest of the team for confirmation.

"It didn't shoot?"

"No it dialed the gate and headed through."

"Did you get the address? They might have some information about my people," Teyla asked joining the briefing late although no one questioned her tardiness.

"I don't think we can walk up to the wraith and ask them,"

Teyla turned her eyes and voice ice cold, "Perhaps not but if we were to capture one," she said leaving the rest up to their imagination.

"Or perhaps it was Michael in the dart and we'd be finding his base of operations." John said giving Teyla a warning look to cool it off or she'd blow her chances.

"Rodney can pull the last 50 addresses and we can search those they should be there."

"I would like to escort some of the teams," Teyla asked looking at Carter knowing John would object but if she could get Carter to allow it she'd get to go.

"If you stay in the jumper I've got no problem with it," John said causing Teyla to turn shock penetrating the mask she normally wore to hide her emotions. She stared at him for several minutes vaguely aware that Carter had agreed and continued on with the conversation. Eventually she heard Carter repeating her name several times and realized that she was still talking to her.

"Teyla I want you to stay in the jumper and do not leave under any circumstances ok?"

"Yes Colonel I understand I will not put myself in any danger," she said coolly unhappy about being talked to as if she we are child.

"I'd like to lead a team back to the planet and see if it was Michael while Rodney gets the addresses am I clear to resume active duty?" John said slightly unsure of where he stood with Carter.

"As soon and doctor Keller clears you go right ahead," she said and indicated that he could go get checked out while they finished up the briefing.

***

Sheppard sat in the infirmary waiting for his test results to prove that he was still healthy. Teyla walked in and waited for her own test results. "Teyla I want you to stay in the jumper and if we come under attack head through the gate don't wait for us just get through the gate alive."

"I understand John you do not need to treat me like a child."

"Yeah but I worry about you we don't want you to end up losing the kid or worse so behave."

"Do not worry John I promise to behave."

"Thanks," he said getting up as he saw Doctor Keller walking across the room. He walked over to her," Hey doc am I good?"

"Yes Colonel try not to wind up here by the end of the day though."

"I'll try," he said laughing as he walked out the door heading towards the armory.

***

He stood before the gate as it light up it had been far too long since he'd gone through the gate. As the gate roared to life he turned and looked up at the control room Colonel Carter, Teyla, and Keller were having some sort of discussion and were looking at him strangely. He stepped through the gate and followed the rest of the team to the village. When he arrived he saw that the city was a smoking ruin he guessed that it had been Michael who had been in the dart and he had some failsafe in place for this kind of scenario. They avoided the city unsure if there were still more booby traps waiting to be sprung and headed back towards the gate where they waited for Rodney and his team to finish.

"Ok got the addresses ready to head back?" Rodney said picking his head up from the computer.

"Yeah dial it up," he said to the Marine near the DHD.

As he walked through the gate he saw a similar sight to the one before he had left Keller, Carter, and Teyla along with Lorne and Zelenka were talking amongst themselves up near the control room. He headed up the stairs with Rodney. As he reached them Zelenka turned and handed him a tablet, "Press play," John did.

"Colonel Sheppard I am truly sorry that I must now abandon you and Teyla in your time of need however I am needed elsewhere for the time being. I understand that you are searching for the Athosians I managed to locate them and have enclosed their location with this message however I warn you that you must act quickly for the wraith have also found Michaels lab and are moving to destroy it soon. I would have given you the planet before but they were recently moved there from another that I had no knowledge of."

"The message ends there and a gate address was sent attached," he said tapping the screen to show them the written gate address.

"How did the ship take off without anyone knowing and when did it take off?" Sheppard asked hoping that perhaps it hadn't left yet or had been stopped.

"We don't really know it doesn't seem to have even gone into space it just seems to have hovered a few feet above Atlantis and then entered hyper-space," Zelenka said excitedly knowing that this would surely shock Rodney.

"It entered hyper-space inside the shield?" Rodney said in total disbelief as Zelenka continued staring at the different sensor readings.

"Yes Rodney," Carter said looking over her own computer.

"But how?" he asked totally confused about how this could happen.

"We don't know."

"I'm sorry to interrupt this but are we going to be launching a rescue mission for the Athosians?" he said and received a thankful smile from Teyla.

"Yes let's compare and see if that planet is on the list I downloaded from the gate."

A/N-I know its really short, and the next one is to, but the next one is also probably the most boring chapter in the entire story. Seriously the whole thing is a briefing. So if it takes a few days for that one to come up, don't worry you aren't missing anything, but the team sitting in chairs listening to each other talking.

Reviews are appreciated.


	20. Chapter 20

Start Chapter 20

The entire senior staff along with several team leaders and other key personnel were also present at the meeting. "Ok Colonel now that everyone is here please proceed with the briefing."

Sheppard stood up in front of them room, "We've located an old city unfortunately its rather large and the life signs are spread out amongst these buildings," Several red triangles appeared on four of the larger buildings. "There are also life signs in sporadic areas around the city and we're assuming those are patrols." He picked up several folders and passed them around to everyone, "we'll be using multiple jumpers," three green triangles appeared on the computer screen, "These will be the escape jumpers when we get the Athosians lead them here two jumpers per evac zone." The military teams will be inserting here, here, and here," he said as three yellow triangles appeared on screen. "We'll also be sending in two teams on the roof tops here and here to provide cover for the teams in the event that you can't get to an evac zone you can retreat up here but we won't be able to get many people out with those jumpers.

"Jumper pilots after you unload your troops you're to head back up and provide fire support for the ground teams," he said taking a seat.

"What kind of terrain is there?" Lorne asked.

"Surrounding the city is a field with some sort of crop growing there. After that it's just forest until the gate the Jumpers will be cloaked a few meters into the forest."

Rodney stood up, "Ok now we need to do this quickly because we've got multiple Wraith Hives with cruisers heading for the planet and they're only a couple of hours out. So once we land we're going to need to move quickly."

"Scientists I know most of you aren't used to front line combat but we don't know what kind of traps Michael has set and the teams are going to need your support so you'll be following them in closely. Once we get the Athosians your to head to these rooftops and board those jumpers." The screen showed the same two jumpers Sheppard had indicated earlier as the emergency jumpers. "Don't worry just do your jobs and you'll get through this." He paused as if unsure of what to say, "I know I'm the last person you'd except to hear this from but if you see some new piece of technology DO NOT attempt to retrieve it we have no idea what Michael has planned and we can't afford to get held up and then the Wraith showing up." Rodney sat down in his chair flipping through the file again.

"Doctor McKay what happens if the Wraith show up and we haven't gotten the Athosians out yet can we except support from the fleet we've been building?"

"Yeah why aren't we using the ships to get the Athosians out?" another scientist asked.

Sheppard stood up, "Because we don't have the time to use our ships believe me I'd love to show the Wraith what we've been doing but chances are the Wraith will have already destroyed Michaels compound by the time we arrive. Our only chance is to go by gate."

"But I thought our ships were faster than Wraith ships?" one of the soldiers asked.

"They are but the Wraith are still right on top of the planet literally only a few hours away our ships aren't that fast." Rodney answered for Sheppard.

"However those who are not taking part in this mission will be taking the ships and heading to the planet in case the Wraith are delayed and we're late getting back in that case yes you can except support from space." Sheppard corrected taking his seat again.

Seeing that they were done and there were no more questions Keller stood up to address her people, "Ok most of you will be going on the evac jumpers we don't know what's happened to the Athosians so I can't tell you what to expect but I don't think it's going to be pretty. Just save those you can and help each other out if you've got to many wounded try sending some to the other jumper in the zone." She paused looking at the ones that would have the harder job, "to those of you who are going with the military teams hopefully you won't be seeing any casualties on our side as the wraith use stunning weapons so pack up on drugs to counteract those effects I won't lie to you though you're going to be seeing the Athosians and you've got to make sure that they live long enough to get back to base where they can receive proper medical attention." She watched their reactions hoping that she'd chosen the right docs for the job. "To those of you staying with me we'll be the safest but we're going to be dealing with a lot of injuries just stay sharp you know how to do your jobs you'll be fine we'll all be fine."

Carter stood up, "I'll be taking the ships so I won't be here to congratulate you guys on a job well done so I'll do it now you're the best of the best and I know you can do this so let's get the Athosians back." She paused for a moment." Godspeed people," She added remembering what General Hammond had told her team several times.

***

Teyla caught up with John after the briefing, "John where am I to go?"

"You're on one of the Athosian evac transports unless you'd rather go somewhere else." He said continuing to walk to the armory.

"No that will be fine thank you."

***

The briefing broke up and everyone headed out to get geared up and headed to their assigned Jumper. It was a big gamble they were betting some dozen jumpers on one operation six to evac the Athosians five to drop the teams in and two to provide over watch for the entire mission. When the Jumpers were ready to go Carter personally dialed the gate and saw the jumpers through before heading up to the orbiting ships and entering hyper-space.

A/N sorry for the boring chapter the next one is a bit more exciting.


	21. Chapter 21

Start Chapter 21

John cloaked the Jumper as soon as it emerged from the gate and flew to the rally point immediately in order to avoid colliding with the other jumpers that were coming in. Him and the two teams in the back waited in an interminable silence as the seconds ticked off the mission countdown. Agonizingly slowly the appointed time arrived and Sheppard followed the teams out leaving the jumper cloaked near the forest. John, Ronon and Rodney headed towards the building with the most life-signs. While smaller than all the other teams his team wasn't attacking it alone far from it and they had Ronon. As his team exited and proceeded towards their rally point in the city Sheppard got a bad feeling and one look at Ronon told John he wasn't the only one. He cycled his radio through the different team's frequencies and heard that they were all pretty much on course and a few others also thought something was wrong.

Ronon returned from his own personal scouting mission, "Sheppard there's a patrol around the corner we can avoid them but we might not be able to find them again."

"How many?"

"Six."

"No we'll get them on the way out. Rodney lets go," he said as Rodney jogged up behind them with his computer and several Ancient devices.

They headed further into the city towards the building. As the Colonel continued to listen in on the other teams channels he heard several teams getting bogged down by patrols. His team however encountered relatively light resistance.

They blew open the door only to find the room completely devoid of life, "Ok Rodney which way?" Ronon asked after clearing the room.

"This way," Rodney whispered motioning towards the door at the far end of the room.

"We just blew open the door do you really need to whisper?" Sheppard joked. Rodney shrugged as the proceeded further into the building. Sheppard was betting this was the building where the Athosians were being held and as he saw the blood streaks across the floor and heard the screams from other parts of the building. They moved silently, quickly, and efficiently towards their objective and eventually the screams were replaced with gunfire and stunner blasts. Sheppard watched as Ronon went around a corner only to reappear again a moment later jumping backwards as stunner blasts whizzed by him. John motioned for Ronon to cross over to the opposite side of the hallway; John poked out from around the wall and fired a long controlled burst down the hallway as Ronon ran across trying to get back behind the corner. John pulled back just as a series of stunner rounds crashed into the wall behind them. Ronon pinpointed the location of the one shooting at Sheppard, Ronon hugged the corner wall and exposing as little of himself as possible angled himself and his weapon around and fired four shots at the target. Sheppard crouched down and leaned around the corner, he emptied half his clip into two of the mutants that he saw. He signaled to Ronon that only one remained; they both jumped out of cover and firing the whole way killed the final mutant.

When the last guard dropped Ronon rushed forward to make sure they were all dead, "Clear."

Rodney ran after Sheppard and Ronon who were already continuing into the facility. However the further they progressed into the facility the more patrols they came into contact with. They were making less and less progress as combat wore on they were hit by stunners and while they managed to stay conscious their reaction time were slower and their progress moved to a crawl before they were finally stalled.

"Major Lorne where are you?" Sheppard said as stunner flew past his head and they all returned fire.

"Yes Colonel we just took out another patrol this definitely appears to be the main building.

"Where are you?"

"About 50 meters from our objective."

"Rodney get me a route," he said indicating for his team to fall back.

"Ok we'll link up with you as soon as we can," John and his team disengaged and sent a grenade towards the enemy. John and his team ran through the facility towards Lorne in an effort to find a path of less resistance.

When they managed to link up the combination of firepower proved effective to break through the enemy lines and make their way a large door. They secured the area made sure that the dead were dead and waited for Rodney to crack the door. After a few minutes they grew frustrated waiting for him to succeed and decided to blast it open. When the charge blew and the door slid open they were met with relief. Many of the Athosians were still alive although not in the best of shape.

"Colonel Sheppard, Major Lorne, Rodney, Ronon where is Teyla?" Halling asked noticing his friend and leader was missing.

"She's waiting for you all in a jumper she's got some news."

Halling nodded and began organizing the Athosians for their escape. After a surprisingly short time they were ready and John proceeded to began evacing them to the jumpers. It was while he was waiting for the Athosians that the entire mission changed twice.

First one of his teams had managed to find and kill Michael. He had been escorted by a number of soldiers when a rooftop team spotted him. They called in air support and took him out with a drones. Sure it wasn't an epic showdown with the heroes like in the movies, but Michael was dead and no one cared how he got that way. With his death the mission seemed to be going perfectly there were reports that several of the soldiers appeared to stop fighting and were surrendering. It was just as the mass surrenders when the first shots hit. The Wraith had arrived earlier than expected and were hitting the planet it was only a matter of time before the darts were swarming over the city.

By the time the darts appeared however most of the teams had linked up and were on the way to the extraction zones. The Athosians had been divided up among three teams each heading to a different zone.

John and his team were heading back across the field to the jumper when the darts spotted them. They dropped several warriors across the field most too far away to be of much concern but a few needed to be dispatched. Sheppard dropped to one knee and began firing at the Wraith while Rodney ran towards the jumper hoping to get aboard. He fired a quick burst at the first Wraith hitting him dead center and dropping him before he could react. He shifted fire to a pair who were slightly off center and loosed another salvo of bullets. The remaining Wraith warriors fell from combined fire from the other teams.

Lorne and his team headed for the second jumper covering Rodney and preparing to guard the Jumper against Wraith assaults. Ronon charged the Wraith closest to the Jumper and held them at bay long enough for another team to get into their Jumper and get airborne. Turning back towards John he headed to him to help hold off the Wraith but John signaled him to head to the jumper. Sheppard turned towards the Jumper and began to stand up when a bright light appeared behind him. It deposited five Wraith a few feet behind Sheppard, the Wraith immediately saw him and fired; the first shot went wide but the second, third, and fourth were dead on. He went down quickly into the grass and several more shots followed him down.

A moment later another white beam appeared behind him this one however deposited no troops it dematerialized him right in front of almost every one of his friends. Rodney stood frozen Ronon fired at the dart and growled. Lorne and his team fired as well and headed to the Jumper. As Ronon ran inside and closed the door Lorne turned patted Rodney on the shoulder as a sign to go and tapped his earpiece "I'm sorry to tell you all but Colonel Sheppard has been beamed up into a dart," he threw his earpiece across the Jumper and slumped down into the copilots chair.

***

Teyla sat in the Jumper listening to the radio communications from all the teams it was boring for her but better than sitting in Atlantis. She heard the news of her people's rescue and then of Michaels death. She was disappointed it wasn't her who'd killed him but at least the man responsible for her people's suffering was dead. She sensed the Wraith as soon as they entered the system the orbital bombardment began almost immediately and ceased only when the darts swarmed across the sky.

All of her concerns disappeared however when the ramp lowered and she saw Kanaan except he was different. He looked at her differently, moved differently, and his face was not his she walked over to him, "Kanaan I am glad you survived."

"Teyla it is good to see you as well," he responded distantly as if she was someone who he had met years ago it hurt her. But she had no time to question him further as more and more of the Athosians came into the jumper many her injured but none severely so. The Jumper became more and more crowded. And she was only able to greet everyone quickly. She was forced back into the cockpit when she heard Major Lorne's voice over the ships comm.. but was unable to hear what he was saying so she turned her own earpiece on, "but Colonel Sheppard has been beamed up into a dart," she stopped her eyes went wide.

He was gone.

They knew the risks Sheppard had told them that if they were captured by the Wraith it was unlikely they would be able to mount a rescue operation. She pushed her way through the packed Jumper—which considering her pregnant belly was considerably difficult-- attempting to get outside she didn't know why but she needed to get outside and see the sky. As she stepped outside the team who were escorting the Athosians were trying to make their way to the cockpit in order to take off.

"Teyla what are you doing? It's not safe out there."

She barely registered the danger, John was gone. They'd grown close again and she couldn't believe that he was taken from her just as she was…just as she was…She couldn't, wouldn't, shouldn't voice that particular feeling. Sure she's always been attracted to him physically and he'd grown on her as she'd gotten to know him as well, but she'd initially given up hope of ever being with him and moved on with Kanaan. She'd doubted his feelings until she'd felt an inkling of them first hand on that ship.

She stood still looking up at the darts as if trying to find the one that had taken Colonel Sheppard. She never heard the Dart or saw the beam but in front of an entire Jumper filled with her people and a team of marines who were standing just inside the jumper she was beamed away.

A/N Hope you enjoyed


	22. Chapter 22

A/N- Only 1 more review and I hit 50, yay. This one is a little short as well, but the next one is much, much longer I promise.

John slowly opened his eyes his vision still blurry from being knocked out. He found himself unable to move any of his extremities and as he looked around the room he saw that it was filled with empty cocoons except for one which contained the only other occupant in the room he groaned at seeing who it was, "Teyla you awake?" he said defeat marring his features of all the people he had to watch die she was the last one he wanted to see die.

"Yes John," she said sleepily she had obviously just woken up as well.

"Dammit it Teyla why couldn't you have just followed my orders and stayed in the Jumper," he asked his anger surfaced not at her insubordination but the fact that he might end up watching her get fed on by the wraith.

She was momentarily confused by his anger but responded with her own nonetheless, "I was not ready to leave you for dead yet."

"Yeah I see how great your rescue plan went either you get to watch me get fed on or I get to watch you get fed on."

"Well perhaps next time I will leave you behind," She said attempting to get her anger under control and make their last few hours civil at least.

"There won't be a next time Teyla I don't see any way for us to get out of here do you?"

"No John I do not," she said her eyes darting around the room looking for anything she hadn't brought any weapons with her because she knew she wasn't allowed to fight. "Colonel Carter should send a rescue team to extract us."

"Doubt it I don't think Carter is going to be sending a team," he said glancing down and trying to lean back.

"Why?" she asked completely confused.

"Well the ship is probably in hyperspace so they couldn't get on the ship even if they wanted to and if we drop out chances are pretty low that any ships are in range."

She looked down trying to think of another possible rescue but was unable to think of one, "I'm sorry John."

"You should have stayed in the jumper with _Kanaan,"_ he spat upset with her and his dislike for Kanaan showing.

"Do you have a problem with Kanaan?" she asked trying to be angry with him, but her it came out as genuine curiosity.

He thought for a few moments looking down he mumbled, "Might as well tell you," he looked up at her their eyes locking; "Yes I have one big problem with Kanaan."

"Why you two have never met?"

"You really have no idea?" he asked incredulously.

"No John I do not," she asked confusion spreading across her face.

"He has something I don't," he said hoping she would understand and he wouldn't have to spell it out for her; he hated to talk about emotional stuff, but she should at least know before they expired. Upon seeing her face he knew that she still did not understand what he was talking about, "You." His voice sounded defeated, he didn't want to talk about it anymore he hoped she'd just drop it.

Her eyes went wide in shock her mouth opened and closed several times as she attempted to say something but found herself unable to. "What?" she finally managed after several attempts.

Her own shock, disbelief, surprise threw him off. "You, Teyla he got you I didn't," he said looking down avoiding her inquiring gaze.

She blinked several times at him still staring at him, "You…You wanted me?"

"Yes. You mean you had no idea?"

"No," she said lowering her own gaze.

"Well I'm glad I never made my intention clearer," he said looking down again trying to accept the fact that the woman he loved didn't return any of his affections.

"Why?" Her mind was still reeling from the idea that he…he wanted her, know he was saying he was glad he'd never told her? They might have had something.

"That would have destroyed our friendship and I wouldn't want to have that," he explained his gaze returning to her face briefly.

"Are you so sure?" she asked her gaze momentarily returning to him in time to see his own confused look.

"Yeah Teyla I'm pretty sure if I'd told you our friendship would have taken a hit, and not one of mine more like one of Ronon's." he smiled at his attempted joke, which fell flat. Now wasn't the time for jokes.

"That wasn't what I meant," now it was her turn to be uncomfortable with the tone of the conversation. As she looked around the holding room, her eyes looking everywhere but at the man to her left, she thought it ironic that of the many places she'd pictured telling him this a Wraith holding cell had never come up.

"Than what did you mean?" he asked earnestly.

"You never asked."

He stared at her total bewilderment written across his face, "What?"

She smiled at him hoping that against all odds Pegasus's playboy would be ready to settle down and…and love her. "You should have asked John I might have said yes."

"Well it's too late now isn't it?" His voice was filled with longing and what-might-have-been. It pained both of them to hear it.

"It is never too late John," she whispered her voice barely audible to the point where she was unsure if he could hear her.

"Thanks but I think after you got pregnant it was a little too late for anything to happen between us," she had no response. She wasn't sure that she would be ready to leave Kanaan, a man who had his own claim on her heart, for John, a man from another galaxy who seemed to have just entered the ring thinking they were about to die, they were the only two men in her life—apart from her father—who she'd…who she'd loved.

***

They'd been left in silence for what she estimated to be about half an hour when she heard something, "John do you hear that?" It sounded like footsteps.

"Yeah I think they're coming to get us," he said as calmly as he could.

"Perhaps it is the rescue team," she said not believing her own words. With one look at John she knew that he felt the same sense of doom that she did.

As the footsteps grew louder she was able to hear three different sets of them. "John it is the wraith I sense them."

"Teyla I want you to know," he started as he heard the footsteps almost around the corner, "That I love you." He'd already pretty much told her but if he was going to die he wanted to say the words to her. He was surprised how much courage imminent death had given him.

She looked up at him and opened her mouth to respond when the lead wraith entered the room hissing at them in order to shut them up. It stood in the middle of the room eying the two. It saw their fear. Slowly it turned to John eying him for a minute before it began to approach him slowly. His tone morose he looked at Teyla, "Goodbye Teyla," he said sadly.

"John," she said desperately as the wraith looked at John up close for a minute before ripping his shirt exposing his chest from which the wraith would feed.

"John I…I," she started but was unable to finish.

He barely acknowledged what she had attempted to say with a look of pure sorrow, "I'm sorry Teyla." He said attempting to come to grips with the fact that they were both dead.

"For what John?" she said hurriedly knowing they had very little time left.

"You're going to die and I wasn't…I wasn't strong enough to protect you," he said lowering his head preparing for the wraith to begin the feeding process. He never heard her response as the wraith forced its hand onto John's chest he finally accepted that Teyla was dead and nothing would be able to save her. After that thought he felt nothing not the wraith draining his life-force he didn't hear Teyla's screams and didn't feel the wraith enzyme flooding his body nothing, just total inky black nothingness.

She sensed the Wraith move away from John and looked up at him but rather than the old grizzled face she was expecting to see she saw the same man who she had been arguing with a few hours before. He looked like he was still alive, "John are you?" however from the way his head was hanging she knew that he wouldn't be answering her. She was totally confused the Wraith had to have fed on John and yet John was still young.

"How did your companion kill himself?" the Wraith asked calmly, curiosity temporarily overwhelming its anger at being denied a meal. She continued staring at John, her eyes locked with his he looked as if he would wake up and smile at her at any second but the Wraith had just told her that he was dead. "How has your companion killed himself?" The voice was angrier now, the curiosity was there but now it was mixed with anger, hate, and fear. What did the Wraith fear?

A/N- Hope you enjoyed, I copied and pasted that last bit from the last chapter to make sure that it was obvious beyond all reasonable doubt that John is dead. Soooo you'll end up reading that again.


	23. Chapter 23

I'm trying a small section that'll be a detour into first person.

Start Chapter 23

She sensed the Wraith move away from John and looked up at him but rather than the old grizzled face she was expecting to see she saw the same man who she had been arguing with a few hours before. He looked like he was still alive, "John are you?" however from the way his head was hanging she knew that he wouldn't be answering her. She was totally confused the Wraith had to have fed on John and yet John was still young.

"How did your companion kill himself?" the Wraith asked calmly as it reentered the room. She continued staring at John her eyes locked with his he looked as if he would wake up and smile at her at any second but the Wraith had just told her that he was dead.

"How has your companion killed himself?" it asked again advancing on her with some kind of syringe in its hand. It approached her again demanding to know what happened to John it stuck the syringe into her arm and smiled, "Your child shall take his place." He said opening the cocoon. She felt the drugs take effect immediately and slumped in unconsciousness.

***

She awoke with a start back in her cocoon. "Your child is becoming one of us." The Wraith said sticking another needle into her arm. "A truth serum," it told her as it released the serum into her blood stream dulling her senses.

The effect was immediate, "I truly do not know what John did to himself," she said fighting the unconsciousness that threatened her, apparently a side effect of the drug.

"You will tell me what I wish to know and you will pay for what he kept," it flexed its fingers preparing to feed on her it wouldn't kill her but take a few years to temporarily satisfy its hunger. She felt its hand on her chest and wondered if minor feeding would kill her child. Then that hit her, her child…her child…he was gone. Tears slipped down her face, it didn't matter anymore none of it mattered, John and her child both gone within hours of each other. Hey eyes closed and she waited for the Wraith to begin draining her life. When it didn't she tried to open her eyes but found herself unable to do so. She considered allowing unconsciousness to claim her but she knew the nightmares that would come with it she fought it.

She managed to get her eyes open for a moment but could not make sense of what she saw. It appeared that the Wraith was on the floor knelling before another glowing humanoid figure. Her eyes closed again and she fought with all of her strength to get them open again but she drifted off.

When she came to she was no longer upright and she was moving her arms were draped around something warm, soft, and…and human. Someone was carrying her! She struggled to open her eyes to see who it was carrying her but she wasn't able to open her eyes. "Go back to sleep you're going to need a lot of sleep in the coming the days," she found herself immediately complying with the mysterious order.

***

When she awoke again she was still aboard the Wraith hive but this time she was in the dart bay she didn't know why the Wraith hadn't killed her or the person carrying her yet but she hoped their luck would hold out. She realized that whoever was carrying her probably didn't know where to take her, "Atlantis," she choked out.

"I know. fear not I will get you there safely now sleep you are going to need your rest but before you do I have one other thing to ask of you."

"What?"

"You must speak to Sheppard immediately please do that first." She again felt her body betraying her and immediately complying with the order to sleep and an overwhelming desire to talk to John, but she realized he's dead.

"D…De," she couldn't finish the sentence as she drifted off again.

***

She awoke again and felt more rested she didn't try and open her eyes at first but when she heard the steady beep…beep…beep of a heat beat monitor her eyes flew open and she found that she was able to focus on her surroundings again. She saw Doctor Keller walking past towards another patient and called to her, "Doctor Keller."

The doctor stopped and turned back to Teyla, "good you're up."

"Did John make it back?" She felt the need to speak with him and despite the ridiculousness of asking if a man she saw die was back she had to.

"Yes how did you two get back?"

"I must speak with him."

Keller looked at her sadly Teyla appeared numb and unconcerned with the doctor's look, "Teyla we need to talk first."

"What about?" Teyla asked still unable to notice the doctor's tone and eyes.

Keller took a deep breath, "Teyla I don't know how to tell you this.

"Tell me what?"

"I'm sorry I'm so sorry Teyla but you…you're…the baby it's...it's gone," she said enveloping Teyla in a hug. Teyla felt overwhelmed for a moment before she felt numb again and unable to feel anything.

"I'm sorry I must speak to John," she said leaving Keller and passing Carter on the way out of the infirmary. Keller stood rooted in place shocked by Teyla's behavior Keller walked over to Carter hoping for some answers.

"Any luck?"

"No Rodney was unable to get the door open and Ronon's method didn't work to well either we've got no idea how he was able to do it but he's locked himself in their pretty good."

"We should tell Teyla," Keller said reaching for her radio.

"No Rodney thinks that if anyone can get in there it would be Teyla he says the door works it's just not admitting anyone in there."

"Then why can't he bypass it?"

"We don't know."

"Did you see her though? She seemed like she didn't even care about her baby."

"I know I couldn't believe it, something happened to them on that ship and I don't think we want to know what it was."

***

She approached his door as some sort of unfeeling zombie. She approached the door and it opened without her activating the sensor. As soon as it opened she seemed to come alive again she looked warily into the room it was pitch black the light seemed to stop at the entrance way and cross no further. She stepped into the room slowly cautiously, "John?" she asked her voice wary. As the words escaped her mouth she felt something surge forward in front of her it was quick just as she sensed its movement she felt someone's mouth on hers. She felt his tongue enter her mouth quickly and a moment later she felt a shock and he recoiled. Light streamed into the room blinding her. It quickly dimmed revealing John standing before her looking slightly embarrassed by his actions. She looked up at him confusion in her eyes.

"Sorry about that."

She felt her mind begin to return to a normalcy she hadn't felt since she'd seen him die but while the foggy haze that had prevented her from thinking was gone no answers had replaced it. She looked up at him hoping he would have some answers for her, "John what happened on that ship? Why am I unable to feel anything for my child? Why did you kiss me?"

He interrupted her realizing she would have still more questions, "Teyla I'm sorry I really am but I'm the cause of your lack of feelings and I can explain the others." She looked at him strangely, "Perhaps it would be easier if I showed you."

He was making no sense to her, "how John?"

He stepped closer to her she felt him exhale, "Close your eyes."

She closed her eyes although she wasn't entirely sure she could still trust him, he was acting very different. A moment later she felt a strange sensation and when it passed she opened her eyes only to find that she was no longer on Atlantis but back on the Wraith Cruiser. As she looked around the room her eyes fell upon the impossible she frantically searched for John eyes wide with fear and shock. She found him a few feet behind her smiling, "John what is this?"

"Watch," he said continuing to smile at her. As she turned to look back at the room she saw three Wraith enter two stayed by the door and another moved towards John. She recognized the words as those the wraith had said just before it had fed upon John.

"John what is this?" She asked confused about why she was seeing this.

"You're reliving a memory your body is still on Atlantis don't worry," he told her walking right behind her she felt his breath on her neck.

As the wraith moved to feed she turned and faced him, "Why are you making me watch this John?" she asked her voice pleading with him to stop it but it continued as she heard herself utter an anguished cry across the room.

"I want you to understand, Teyla, I need you to understand."

"What about the others?" she asked realizing she didn't know how Rodney and Ronon had made out in the rescue operation.

"They can find out in other ways later, but I need you to understand first."

"Why me?"

He smiled at her as he took a few steps away from her. Teyla saw the Wraith reenter and inject her with something. She saw herself slip into unconsciousness and knew that this was the last thing she had a clear memory of. She was dragged out of the room, by the two lesser Wraith. She followed her body through the Wraith ship finally ending up in surgery.

***

The Wraith stood over her admiring the knife, newborns were a prized commodity among the Wraith, they had such life force to give_._ Teyla was shocked to hear the Wraith's thoughts. "Kind of scary the first time isn't it?" John asked from behind her. "Hearing their thoughts, they're so weird." He gave her his charming smile in an attempt to disarm her. She turned her attention back to the scene.

The male may have died, but he intended to savor this newborn. He moved over to his "patient" a wicked smile playing across his face. He lowered the scalpel to her bare belly. On the verge of making his first incision he growled when he heard another approach. "Forgive the intrusion commander, but the Queen has ordered you to not feed on the child." The minion paused for a moment afraid that the scalpel would end up in his neck. Seeing that it wasn't he quickly continued, "We have learned much from the hybrids research and she wishes to test it out on this one."

He hissed at the minion, "Bring me the syringes with his formula and I can have it finished within the hour." He turned back to Teyla's body and growled.

***

After another couple of minutes in which nothing happened the three wraith reentered and one approached Teyla while the other two stayed by the door. She saw the lead wraith approach her it looked as if it were preparing to feed. She looked around to find John and noticed that he was several feet away from her now. Out of the corner of her eye she saw Johns body encased in the cocoon still. He appeared alive and well—if acting strangely—but he was definitely dead in that cocoon. She stared at his face it looked like he still could have been alive she imagined it was still warm. As her eyes came upon his—the living one standing off to the side-- she smiled slightly knowing that he was still alive. She sought him out wanting to make sure that he was still alive and she wasn't dreaming; that they had in fact escaped this nightmarish ship. She looked around and saw that he had moved far away from her for whatever reason she looked back over to the dead version of him. She walked towards the corpse slowly as if afraid she would change history, her eyes searching everywhere on him for a sign of life. When she was a few feet away his eyes burst open exploding with light. She jumped back as tendrils of light escaped from his eyes she saw that the rest of his body seemed to be glowing as well. The cocoon exploded a moment later giving her a good look at his naked arms which appeared to be glowing slightly. "John?"

"My body is partly ascended. Energy is flowing through me," he answered from across the room as the other John stepped out of the cocoon to the shock of the wraith. The one that had been about to feed on her stepped back and moved away from John the other two raised their stunners preparing to fire. John's head snapped to them and he hissed at them as they fell to the ground dead.

The other wraith fell to its knees something she knew wasn't voluntary by the look in its eyes John walked slowly over towards it; when he was right in front of it he looked at his hand. He inspected it staring at his palm and then turning it over and continuing to stare at it he closed his eyes and bowed his head for a moment. When he opened his eyes again the skin appeared paler and a faint smile appeared on his lips he leant down next to the wraith and whispered something into its ear. Teyla watched the wraith and for the first time in her life she saw a wraith tremble in fear. She heard the wraith cry out in pain a moment later. She looked at the wraith confused as to what was causing it pain as her eyes crossed its chest she saw something she never thought she would Johns hand feeding on the wraith. She spun around to face him he had anticipated her move and was already holding up both of his hands palms facing her showing her that he was not a wraith, "I can change my DNA at will," he explained.

"Where is Colonel Sheppard?" she demanded of him.

"I told you to call me John when were off duty and I'm right here," he said as the world around them froze.

"You just told me you can change your DNA. John cannot," she advanced towards him angrily.

"Teyla it's me John."

"Then prove it tell me something only he would know," she demanded closing in on him.

"Like what? Missions? First meeting? Final words?" he asked knowing that he would be able to tell her everything but not whether any of it would satisfy her.

"What was the last thing he said to me?" she said continuing her advance on him.

"I apologized for not being strong enough to protect you," he said smiling at how wrong he had been.

"What was the first thing you asked me when we were alone?" she asked stopping her advance towards him.

"If I looked through you," he smiled remembering when he had no knowledge of the wraith and none of the memories that he was now burdened with.

"What did you say to me on the Daedalus on the way to Sateda?" she asked taking a few steps back away from him.

"That you were all family to me," he said hoping that this was her final questions.

"Who are you that you know these things?" she asked again standing a few feet from him.

"Teyla it's me, John, but perhaps you should continue to watch," he suggested as the scene moved forward again.

She turned and watched as the wraith fell back dead and John slowly moved over towards her. He whispered something to her quietly she could barely hear it but she knew it wasn't any language she had ever heard before. He then placed his hands on her, closed his eyes and bowed his head. She saw an incision on her belly heal immediately.

He continued smiling at her as a white light began to surround him. It was similar to when she had witnessed ascension before but different he was maintaining his human form, "John?" every time she asked a question she simply became more confused. As his body became light she saw something she had never heard or seen before multicolored bands began rippling around and through him. "In simple terms Teyla I am ascended I am the reason you got off that ship, can't feel anything for your son, and the reason you felt the need to speak to me."

"Why did you do that?"

He approached her slowly and spoke with a quiet affection, "Because I never could allow harm to come to you."

She took a deep breath preparing herself for the conversation she was about to have, "What are you?"

He smiled at least she hadn't run away screaming she was handling this better than he expected, "You know the ancients ascended to a higher plane of existence right?"

"You are an ancestor?" she asked skeptically some of the powers he had demonstrated she had never heard of the ancients possessing.

"No. The ancients inhabit one plane of existence now I inhabit another one."

"If you are ascended why do the ancestors not stop you?"

"They can't, they've tried before and failed," he said his eyes dimming as he remembered when the ancients had last attempted to stop him and what he had had to do in order to prevent them from doing so.

"They failed?" she asked in total shock that a species as powerful as the ancients could fail to stop one man.

"Yes I inhabit a much higher plane than the one the ancients inhabit and because of that my power is much greater than that of the ancients. I can answer the rest of your questions when this is over please watch," he asked as her memory resumed. She nodded and turned away from him. The wraith was on the floor dead and he was walking towards the cocoon that she was trapped in. She was still unconscious as the cocoon opened and he approached her. A look of concern flashed over his eyes as he saw her condition he placed his hands on her and closed his eyes again. "I needed to heal you I'm sorry I couldn't save your child."

"Why couldn't you?"

"The Wraith experimented on him, he wasn't human anymore."

"You can change your DNA, why cannot you not fix my son?"

"I can't change another's DNA. To do so would violate some of my highest laws."

She realized she wasn't feeling much of anything for her son, no grief. "You are still blocking my emotions?"

"Yes," he said as she turned back to the cocoon where John and finished healing her. He then gathered her in his arms and left the room heading for the dart bay. She realized that when she had woken up she had been in his arms as he carried her out of the ship. Her thoughts were interrupted when he spoke to her again, "Would you like me to stop?"

"Stop what?" she asked as he approached her.

"Inhibiting your emotions," he said standing in front of her staring into her eyes.

She was surprised at his willingness to stop she had expected to have to demand that he stop but now faced with the choice she wasn't so sure, "I…I."

"You don't have to decide now," he said as she looked up into his eyes. She found herself unable to look away as the world faded around her to be replaced by his quarters on Atlantis.

"I must leave I have business to attend to and you must be tired," he said moving to the door. She turned slowly suddenly feeling as if she hadn't slept in days. "You can sleep here if you want I have no need for it any longer," he said as he walked out the door closing it behind him. She stood their speechless she wanted to see her people but she was exhausted and the bed looked so very comfortable.

***

_Several hours later_

"Rodney look at this," Sam said looking at one of the control room screens while Rodney was busy with the long range sensors.

"Yeah it's our power usage to output, looks normal," he said arriving at the console tablet in hand.

"Look at the output," she said tapping the screen where the output reading was.

"What? That's not possible," he said a mixture of surprise and fascination in his voice about the impossible readings.

"That'd be about what 10 or 12."

"It has to be some sort of error I'll have someone run a diagnostic," he said tapping a few keys on his tablet to confirm the data.

"Rodney I don't think it's an error," she said looking at the screen.

"Why?" he said looking up at the screen, "now that's impossible what could possibly be using that much power." He said seeing that their power consumption had increased to almost match their new power output.

"I don't know but let's start running every diagnostic we can."

He began walking away when both of their radios came to life, "Please meet me at the top of the control spire in five minutes," they heard Sheppard say.

***

They stepped out of the teleporter eager to find out why Sheppard had called them here. They stepped out on the balcony and saw Sheppard his back facing them hands on the railing, "Hello Doctors," he said mysteriously.

"Colonel why did you call us here?" they asked approaching him slowly.

"Your questions about the power usage," he said still staring out into the city.

They stopped a few feet from him, "What about them?"

"Would you like the answers?" he said slowly removing his hands from the railing and letting them fall to his sides.

"You know what's causing it?" Rodney asked as Carter took another step towards him.

He turned around slowly, "Yes," his body was bursting with energy. As he faced them they both jumped back away from him.

"John what is happening to you?" Carter asked trying to sound as friendly as possible.

He smiled at her as more of his body was converted into energy and bands of energy appeared around him. "Come I wish to show you something," he said moving through them and heading towards the teleporter they had just left out of. It took a moment, but they both realized that John was now ascended.

"What?" Rodney asked again following him.

"Get in," he ordered brusquely stepping into the teleporter.

"Where are we going?" they both asked stepping inside. He didn't answer them and instead just tapped the screen activating it.

***

They emerged from the teleporter in a seldom used section of the city. "We're by the hyperdrive engine," Rodney commented emerging from the teleporter. John continued down towards a staircase Sam and Rodney followed now sure that something was happening with the ships drive but still unsure of what exactly was happening. They followed him silently down two flights of stairs arriving at a rarely used door.

He turned and faced them standing just in front of the door, "You wanted to see where all that extra power is going?"

"And where it's coming from," Rodney added as Sheppard opened the door and stepped inside. The room was spacious and contained a number of screens and a large window which overlooked the previously empty interior of the spike. They walked to the window and looked down into the interior, "What is that?" They asked looking down and seeing a shimmering energy field.

"That is a shield and where your power is going," he said moving over to the nearby controls and looking at the readouts. "To be more specific it's the tertiary shield a backup in case the first two fail."

"What are they there for?" Carter asked moving over to the readouts while Rodney remained at the window.

"Containment procedure and to use up all the extra power," he answered adjusting a few of the controls.

"What kind of containment is this?" Rodney asked now looking at the readouts as well.

"A three shield containment system the first shield is sustained long enough for the second shield to build up a charge at which point it takes over the containment and draws enough power to sustain itself while the third shield exists solely to protect Atlantis in the event that the second shield fails."

"But what is it containing?"

Sheppard smiled at them as the third shield faded and was replaced with the first shield surrounded by a thin second one. Looking at the readouts they saw that this was where all of their power was going although they still had no idea where it was coming from. He turned to them, "Watch and keep your minds open to all possibilities."

They walked over to the window and stared down as John moved behind them. With their attention firmly focused on the shields they didn't notice as his body turned into energy as he began ascending. Noticing the light behind them they turned to look at its source, "Sheppard what are you doing?"

"I will explain later now watch the shields this is something you two don't want to miss," he said and they slowly turned around still eying him but trusting him enough to turn around. A moment later they saw a flash of light and energy washed over the first shield which held for a moment as the second shield flashed a bright green a moment later the first shield collapsed and the light in the center expanded to meet the second shield which held.

"What is it?" they both asked still staring at it.

"A White hole," he said standing next them appearing fully human again.

"But…But those…they don't exist," Rodney sputtered while Carter having more experience with the impossible remained silent.

"Normally yes but I am not subject to the same laws that you are I can break them and follow them at will. When designing Atlantis I decided on many security measures to make sure that the power this provides would not be abused and the shields would be safe from damage and tampering."

"Where is the power for the shields coming from?" Carter asked as Rodney stood in silent amazement.

"Extra ZPMs that are heavily secured. With this power however you will be able to run many additional systems including the full defensive and offensive systems."

"Wait Atlantis has weapons beyond that of drones?"

"Yes drones are nothing compared to what a fully powered Atlantis can fire."

"What are you?"

"I am ascended,"

"Why don't the ancients stop you and how do exist like that? Orlin couldn't." Carter asked looking at the screens again and seeing how much power her teams would have to use for their experiments.

"They tried once and failed miserably so we've reached an understanding. As for Orlin, well my kind are able exist in both states simultaneously the Alterans are not able to do so."

"You defeated the Ancients?" Rodney asked in disbelief.

"Yes would you like me to explain our history?"

"Yes," Rodney answered immediately.

Sheppard took a breath in preparing for his response, "There are many planes of existence the Ancients inhabit an ascended one. I inhabit a much higher ascended one because of what I am I can understand more of the universe than the Ancients can and I can exert more control over it. I believe in interfering on the lower planes this as you can imagine was a point of contention between us. When the war against the wraith started they allowed me to participate but as more and more began to ascend and they decided that I shouldn't be fighting in the war anymore and attempted to stop me. I resisted and they failed, some died in the fight but most survived. They knew I didn't want to fight them but I knew they couldn't defeat me so we struck a deal where I wouldn't interfere for a time and then I could interfere without their opposition."

"So we just got lucky that now all of a sudden you can do whatever you want?"

"Not entirely the Ancients can still oppose my actions, which is why I have not wiped out the Wraith yet. Colonel Carter could we use the conference room as somewhere to review my actions?"

"Why would you have it here?"

"Atlantis was their capital city and some still have a certain fondness for it."

"No why here on this plane?"

"Well you will have a say in the matter of course and so it will be held here."

"Oh we're going to have a say in this?"

He moved towards the door opening it with his gene, "Of course we would not act without your consent."

"Who will be representing us?"

"That is your choice," he said heading back up the stair case and towards the rest of the city.

They remained down in the observation room for some time simply absorbed in the energy readouts and the impossible singularity that was now powering their city. After syncing the tablets with the Ancient machines they headed back up the stairs following the path John had lead them down hours before.

A/N- More should be clarified in future chapters. Hope you enjoyed, and in the event you didn't realize yes this is the Secret that the title refers to. I might update this in the future if it's unclear so let me know.


	24. Chapter 24

A/N-There's really no excuse for how remiss I've been in my author duties so I won't insult you by providing any. Sorry I waited so long, I'll try and update this story again when I wake up from jet lag recovery.

Chapter 24

"Teyla are you in here?" Morgan called from the doorway.

"Yes who is it?" Teyla called from somewhere inside the room.

"I am a friend of Johns I need to speak with you."

"Come in," Teyla said appearing in the door and welcoming Morgan in. "I'm sorry but who are you?" Teyla asked again as Morgan walked in and took a seat near John's computer.

"I am a friend of John's, an Ancestor and your personal representative John told me to get to know you so I came to find out about you," She answered casually looking at the bed suspiciously.

"My personal representative for what?" Teyla asked taking a seat next to Morgan drawing her attention away from the bed.

"The council which will vote to approve or disapprove of John's actions now would you mind if I asked you a few questions some will be personal others professional."

"I suppose you would need to ask them wouldn't you," Teyla said taking a deep breath in preparation for what she was sure would be many deep and penetrating questions about her life from an Ancestor no less.

"Why are you sleeping here in John's old quarters?"

"He told me he had no further use of them and I was free to sleep here if I wanted to and I have been exhausted for the last few days so I remained."

"Do you fully understand what happened on the hive?"

"Yes I believe I do," Teyla answered shifting in her seat.

"Do you remember everything John said to you in both ascended and unascended forms?" Morgan asked looking through some of John's computer files.

"Yes why?"

"I care for him greatly he is a great friend of mine and I simply wished to make sure that you were aware of everything that is happening. I do not understand why he has chosen to withhold some information about himself but I sense that you already know part of it," Morgan scanned through several of the computers files looking for something. "Why have you not asked him to stop interfering with your mind?"

Teyla sighed it looked like the questions were starting to get harder again, "because he is blocking out the negative emotions that I do not wish to feel and I trust he will not use that power against me."

Morgan opened a large file only to find it password locked, "Who was the father of your child?"

"Kanaan," she asked standing and heading towards the kitchen where she knew John stored some bottles of water.

"Does he know about any of what has transpired recently?" Morgan asked when Teyla reentered the room with two bottles of water.

She stopped dead in her tracks as the realization that Kanaan was not only alive but on Atlantis sunk in. she really hadn't been thinking about him the last couple of days but she had forgotten to tell him about anything she had been so wrapped up with John and then she felt like she had slept for an entire day at least.

"I'll take that as a no, has Kanaan ever told you he loves you?"

"I…He… Yes he has," she wanted to tell her the entire story but Morgan didn't seem interested.

"Ok I've got a job to do and I must admit these questions aren't the most helpful so I'm going to ask you one last question about this before I ask you about the rest of your life ok?"

Teyla nodded, "Yes not that I appear to have a choice in the matter."

"Do you have feelings for John?"

"I…I…I am," Teyla started before looking into Morgan's cold eyes which gave her an idea, "Yes," she wasn't lying of course she had feelings for John those of a friend and Morgan hadn't specified which kind she meant. She wasn't entirely ready to tell anyone any more than that.

"How old were you when your mother died?"

"Five," Teyla answered smiling at her avoidance of the previous question.

"Your father was taken how many years ago?"

"Eight."

"You joined the Atlantis expedition because they were your best hope of fighting the wraith correct?"

"Yes," she answered beginning to get uncomfortable again with Morgan's questions.

"Would you leave again and join your people never to contact Atlantis again if the Wraith were defeated?"

"I would join my people but I would want to remain close with Atlantis."

"Would you move into the city with all of your people if given the chance?"

"Yes," Teyla answered quickly and firmly.

"Do you know what John's password is?"

Teyla laughed she had known Morgan was trying to get into John's computer for some time now and based on the keys her name had been entered several times, "Try football."

"Thank you," she said as the file opened up. "You appear to have adapted to life on Atlantis quickly."

"Thank you."

Morgan was absorbed by the document whatever it was Teyla knew she would need to read it as well, "I have no other questions do you have any for me?"

Teyla had been surprised when an Ancestor had come to John's room to ask her some questions but now being able to ask her anything it was unbelievable, "Yes can I sit in on this meeting?"

"Yes."

"Why did John take human form?"

"That's something for him to tell you," her cryptic response didn't answer her question but she moved on regardless.

"He's going to have to leave after this is over isn't he?" Teyla asked as she sadly realized this wouldn't last forever if it lasted longer than a week she would be surprised and she would miss him he had been her oldest friend on Atlantis.

Morgan stopped with the computer for a moment sensing the emotion in Teyla's voice, "Yes he will but I am sure he will return to you."

"When is the meeting?"

"One thirty in the conference room," Morgan said getting up. "Any other questions?"

"No."

"I must go then I will see you at the meeting Teyla."

***

Morgan had gained an insight into Teyla's thinking but that hadn't been the reason for her visit or questions. She knew beforehand where everyone would be voting there were a few votes that might shift but only on some very radical issues something she hoped would not come up. The point of her meeting had been to get a better feel for who Teyla was and the nuances of the language hadn't been lost on her especially when she herself had been using some of the languages faults to her own advantage. She had sensed when Teyla had gotten annoyed at the quick pace of the questions and the fact that Morgan had not allowed her to explain any of her answers and reacted accordingly. As she emerged she was uneasy about the trust and power John had given the Athosian but she did at least seem to be worthy of them and Morgan did not look forward to ever being on the opposite side of the negotiating table of her. Of course she had the brief on her and known many of this in addition to every mission report anyone had filed including Teyla's.

After answering several questions Morgan grew disinterested in Teyla's answers and had looked to John's laptop he had used it once or twice since he had reascended but she hoped it might provide some better understanding however the computer had some sort of code. Her time among the Earthlings hadn't exactly shown her how to best break the code but the code would have been conceived on Atlantis where no one would be trying to steal his data and he wouldn't have come up with a long password just something easy to remember. Speaking to Teyla had eventually become just a cover for her to get the password and unlock his computer fortunately she had managed to do so rather quickly but she ran into another problem when one of his most recent files appeared to be further protected and those she had been unable to access for some time until Teyla have given her the password. With the football password she had been able to finally access the document she hadn't considered that John would have used something from his human form as a password. She then proceeded to read through the document quickly and then left.

***

After allowing the three delegates to settle into their temporary quarters he had gone for a walk and ended up on a balcony right on the ocean. It was one of the lowest he knew of and the spray from the ocean occasionally drifted up to it. He smiled as one of the larger waves sent a great deal of mist into his face it felt good. He sat there for some time when he felt Morgan approach from behind, "You spoke with her?"

"Yes, how much have you told her about yourself?" Morgan stood next to John relishing in the cool water herself.

"Not that much about half of what I've told you," he shrugged knowing Morgan would want him to tell her everything.

"She trusts that you won't use your power for more nefarious purposes," Morgan sounded surprised but as she thought about it she realized that Teyla had nothing to fear from John.

"You didn't ask about her life and opinions did you?"

"No I did just not ones that will be effecting the council," Morgan smiled realizing John had known what she was going to ask all along he was as sharp as she remembered and he seemed happier then she remembered.

"I just hope you know what you're doing," he moved away from the railing.

"And I you," she said smiling as the door parted. "John," she waited until he had turned back around before finishing, "don't forget about yourself."

He laughed and walked through she knew he would ignore what she had told him. After all those years it seemed the one thing he hadn't learned was that sometimes others had good advice. She stayed there for a few minutes enjoying the ocean before returning back inside.

End Chapter 24


	25. Chapter 25

Start Chapter 25

Teyla waited for the rest of the Ancestors to leave before standing and talking with John and Ganos. The council meeting had been very boring and Ganos and John had explained that it was a mere formality with everyone already knowing what measures would pass and who would be voting for what. She had decided against returning the next day but the third and final session she had been promised would be more interesting. After they had departed leaving John, Morgan, Daniel, General O'Neill, and Mr. Woolsey she stood and moved towards John and Morgan. "Sheppard thanks for the help there," O'Neill called from across the room.

"Thank you John and Morgan," Teyla said more respectfully towards the pair.

"Oh it was nothing a few basic measures and some other boring stuff. Daniel if you want we can discuss your ascension later and I've got a few other things you will be very interested to see."

"Ok what time?" Daniel said gathering his many papers on which he had written notes.

"John I will speak with you later and Daniel I look forward to speaking with you as well," Ganos said quietly leaving through the doors. Daniel, O'Neill, and Woolsey departed heading out to relax and take in the city or work on more ancient research in Daniel's case.

"Why do some of the ancients oppose you?" Teyla asked as she took a seat next to John.

He sat next to her, "Because they feel that it isn't right it's more civil now they've accepted that I'm going to do some of this stuff and are just opposing to look good and avoid looking like a hypocrite."

"So why does Morgan or Ganos support you?"

"She and others like her have taken my position and believe that it is sometimes necessary to interfere in the lower planes," he voice was quiet and he seemed happy to retell his history with the Ancients.

"Why did you adopt that position?"

"It was taught to me by my creators," a sad smile spread across his face as he remembered them.

She thought for a moment about what Ganos had told her about his influence, "John you offered to stop interfering with my mind and told me that you would do it whenever I asked correct?"

"Yes I will stop immediately however in case you ever wish to escape I will allow it to continue in my old quarters to which you have free and unlimited access of course. Unless you are bothered by me allowing it to continue there? It will take some time to wear off."

"No and thank you for stopping John," she rose from the table and headed towards the door she paused at it for a moment and turned back to him, "Good luck tomorrow."  
"Et tu and thank you," she disappeared through the door leaving him alone in the conference room.

***

As she approached her quarters it dawned on her that she hadn't been in there for days. When she opened the door it was just as she had left it. The meeting had been long and it was already late at night but she wasn't tired and decided to finally seek out her lover Kanaan. She headed for the quarters she had learned he was assigned. She quietly opened the door and entered his quarters she found that he was still awake laying on his bed. "Teyla I have been looking for you it is good to see you."

"Kanaan I am sorry I have been busy," she said taking a seat on a chair next to his bed.

He sat up and moved over towards the chair, "I am just happy to see you again."

"I was…I...We…I lost our child," tears formed in her eyes and streaked down her face.

He sat there for a moment in utter disbelief at having a child and then losing it. He looked up at her again, "We will get through this," he gently wiped the tears from her face. "Won't we?"

She sighed he was always so unsure of himself, "Yes." He brought her into their first kiss in many months and she reciprocated happy to finally have him and her people back safely in Atlantis.

He broke the kiss just as she had moved to deepen it, "When should we have the bonding ceremony?"

Her face dropped and she leaned back into the chair sighing, "I…I…I do not know."

He withdrew back towards the bed confused he had been so sure that she wanted to be to be with him. _Perhaps it has something to do with where she has been in the past few days?_ "Teyla where have you been these past few days?"

She blushed realizing immediately how it would seem to Kanaan with her rejecting him and having spent the last few days in John's quarters. She looked up their eyes locking, "I have been around I have spent much time learning from Colonel Sheppard."

"What has he been teaching you?"

"Of himself he fought against the wraith with the Ancestors he has learned much of the years and sacrificed much in those years."

He nodded accepting her answer, "Where are you sleeping tonight?"

She smiled at him knowing what he was really asking, "In my quarters." She gave him another quick kiss and stood up to leave. He scrambled out of bed behind her, "Alone," she added with a smile.

***

After visiting the other Athosians she retired to her room and as she lay in bed remembering Kanaan she felt an unusual emotion tug at her heart. She tried to ignore it and get some sleep however it ate away at her. She did not understand why she felt guilty but she felt as if kissing Kanaan had been a mistake. "Morgan," the name was out of her mouth before she could even think of why she needed her. Her door chimes sounded a moment later and the eerie realization that everything she was doing and saying was being monitored by Morgan hit her. She opened the door and admitted Morgan entrance, "Is this what you were referring to?"

"Yes, I understand your actions and so will John however that will not lessen the impact it will have on him."

"What if…What if…No never mind," she closed her eyes and leaned her head back against the wall.

"What? I'm here to help you if John or myself can help you need only ask."

"Do you know what I feel?"

"No, John would never allow it."

"I feel guilt but it does not make sense to me I have no reason to feel guilty for being with Kanaan."

"Teyla I don't know everything about you but I think I know enough to know that perhaps you have or had feelings toward Colonel Sheppard," Morgan's voice was quiet almost a whisper.

"He is no longer that man even if I had feelings for Colonel Sheppard that man died on the Hive."

"No he didn't Teyla and we both know that the Colonel and John may have had differences but they both profoundly affected each other and are remarkably similar. The only real difference is the way John's past has affected him."

'What are you saying?"

Morgan smiled and stood, "You know what I'm saying and I cannot help you with your decision it is your own to make."

"He still has feelings for me?" Teyla asked nervously unsure of what answer she wanted to hear.

Morgan turned in the doorway and smiled, "Yes."

Teyla returned to her bed after the door closed she felt more at ease with Morgan than she had ever thought she could.

As she drifted off to sleep her dreams were filled with John and Kanaan. She knew that she was being forced to choose between two men whom she cared for deeply.

End Chapter 25

A/N Wow considering how short this chapter is I feel kinda bad not posting it with the previous one or the next one.


	26. Chapter 26

Start Chapter 26

"Doctor Jackson?" she asked from the doorway.

"Yes come in," he called from the balcony despite not knowing who it was.

"It is good to see you again Daniel I'm glad you made it out of the Ori galaxy safely," Morgan entered slowly onto the balcony where he was admiring the view.

"Thanks for the help there," he didn't really know how to react to her presence, she had sacrificed herself so that the Ori could be defeated. They stood there for a moment admiring the view in silence. "Did you know he would help you?"

"No and neither did Oma if you were wondering."

"Oma is free again?"

"Yes and continuing with her old ways already," John added walking onto the balcony drinks in hand with Jack following closely behind.

"Sheppard what do we call you?"

"Anything you like although I would ask that you don't refer to me by my former rank."

"Ok Homer what are the drinks for?"

"We wish to celebrate you for defending the people of galaxies you have done everything we could have hoped for and now I shall join you in this fight and end it," Sheppard said raising his glass.

"To the Tauri," Morgan said raising her glass.

"To humanity," Daniel added.

"To peace," Jack said finally raising his glass.

"To peace," they all echoed clinking their glasses together.

"Sheppard you wanted to discuss something about when I was ascended?"

"Yes I apologize for not helping you had I known that Oma would ascend someone during that time I might not have left my home plane," he took a sip of the champagne resting against the balcony as everyone admired the city as night.

"What you were doing your own thing and it wouldn't have mattered I still would have interfered."

"It worked out for the best in the end,"

"Yes but I wish it had not cost so many of your people's lives."

"Well you're here now Sheppard,"

"Do either of you have any questions for me?"

"You mean we can just ask?"

"Yes I will be happy to answer them you are the ones who will need to explain it to your leaders who will explain it to the rest of your people."

"Yeah I don't know about that we aren't exactly telling everyone about the program."

"You will need to after this is over," John and Morgan shared a knowing look as they watched some of the rooms lights activate.

"Why?"

"Don't worry I will be there to secure a safe painless transition."

"What happened between you and the ancients?" Daniel asked them quietly as O'Neill continued to take in the sights of the city.

"I interfered in the affairs of lowers they disagreed and at that time they were new to ascension and felt that they could do anything however they weren't nearly as powerful as I was. I was eventually forced to kill some of them and after that conflict our current arrangement was negotiated."

Morgan looked solemn she hadn't been there for the conflict but she remembered what it had done to the ancients who had survived.

"Sheppard what exactly are you planning?" O'Neill asked turning and facing the room as he heard someone at the door.

"Wipe out the wraith and return this city to its former glory," Sheppard said stepping inside and went to open the door.

"Sounds nice," he said as Sheppard walked back out onto the balcony.

"General," Sam said as she walked out onto the balcony.

"Carter how's Atlantis doing?"

"Good Rodney's still working on getting his hands on every system he can."

"Don't worry neither he nor Atlantis are in any danger," John said smiling as he established a mental connection with lanti.

"I wasn't he's quite fascinated by her by the way."

"Yes he is," Sheppard said smiling.

"Daniel come I have something you might want to see," Sheppard said as he headed into the room with Morgan. Daniel followed them out leaving Sam and Jack on the balcony.

"Well it sounds like I'm going to be out of the job soon,"

"Oh really?"

"Well it appears home world security is about to become obsolete and with the paperwork I have to do for the security of one planet I'm certainly not going to do it for an entire galaxy."

"So you're going to retire again?"

"That's the plan finish up with these and then straight onto blissful retirement," he smiled out into the city.

"Going fishing?"

"Of course Carter care to join us?"

"Us?"

"Me, Daniel and Teal'c,"

She smiled, "Have you put fish in the lake yet?"

"No, I hardly ever get to head up there."

"Any other plans for retirement?"

"One or two," he smiled at her.

"Oh like what?"

"I think I'll wait until I'm retired before finalizing anything and speaking of retirement I think I will retire for the night."

"I'll see you tomorrow General," she finished off her glass and turned to head back inside.

"Goodnight Sam,'

"Goodnight Jack,"

***

"What is this place?" Daniel asked as they entered a cavernous room.

"My personal study," John replied indicating the books on the walls.

"It's normally heavily restricted I have only been in here once or twice myself," Morgan said heading over to the staircase to the second floor.

"I'm giving you total and complete access to the first two floors the third floor will remain completely sealed off," he followed Morgan up the staircase to the second story.

"Do not take it personally no one has ever been allowed onto the third floor," Morgan added standing next to a portrait of the first Ancient to ascend.

"The information contained in those archives is not for those as young as you."

nodded looking up to the third floor which seemed to contain a much greater amount of dust than the other two. Morgan walked next to him, "This is a great honor he only trusted a few of us to use the first floor."

"If you're ascended can't you see what's there?"

"No he shields certain areas and people from us."

"So what do you think is up there?"

"I believe its records from detailing his creation and some of the deeds he has done which now haunt him."

"Then why do you keep them here? Who are they for?"Daniel asked intrigued by those books.

"I have to keep them somewhere and I have a certain fondness for this place." He headed over to the nearest set of books and grabbed one heading over to a nearby chair. "Enjoy Doctor Jackson."

"You're not staying?"

"No I have other business to attend to however someone will come and collect you shortly before the next session," he stood in the door waiting for Morgan to leave.

"Good luck Doctor Jackson," she said departing from the room.

"Enjoy Daniel," the door shut with a thud behind John as he headed back towards the center of the city.

***

They sat down on a balcony on the edge of the north pier, "How have things been since I left?"

"Not well I hoped to avoid any interference but I was exiled," she leaned over the balcony as a wave crashed into the city a few feet below.

"I'm sorry if I had known that the Ori were going to be alerted to the Milky Way I would have dealt with them," his eyes darted to the corner where Lanti appeared joining them.

"Think nothing of it my exile is effectively over and you're finishing most of what needs to be fixed at this point."

He smiled at her, "Thanks but I have so much to do still Sateda and of course setting up a government.

"You intend to attempt to do both?" she breathed in the salty air missing Atlantis's original homeworld.

"I need to give back some of what this galaxy lost which won't be easy but I think I can get it through and as for the terra populus well they need to take their place as leaders." Lanti moved over and sat on John's shoulder her usual place able to whisper into his ear should she need to and able to look at others easily.

"You think they are ready?"

"Yes they had the guidance of the Asgard, Nox, and of course your own limited guidance," he got up and moved towards the door.

"I will of course also be helping them regardless of what the Alterans think," Lanti added as John and her moved inside.

***

"How have you been Lanti?"

"Well enough John I have been dark for most it and I hid from them when ZPM's were activated the Asurans were quite persistent in seeking me out the Alterans less so," Numbers flashed across her.

"What are you doing?"

"Charging up the inertial dampeners and using automated repair facilities to repair some of the remaining damaged sections of the city."

"Eager to return home?"

"Yes especially since I'm now allowed to have full power again."

"I've been thinking you've been on your own for a long time and didn't destroy anything," she looked up at him her eyes filled with excitement. "Perhaps you're ready for the responsibility of handling Atlantis's more advanced weapons."

She beamed having waited for the opportunity to do so since she was first brought online, "Thank you John I won't disappoint you."

"I assume you're familiar with the access code?"

Her image disappeared giving him the answer.

End Chapter 26


	27. Chapter 27

Start Chapter 27

Did some editing, everything is going up tonight. My apologies for my horrible updating.

John leaned back in his chair preparing for the council to break for the day.

Johns eyes wandered over to Novious who was smiling something that always made John uncomfortable. "Ancient we did not wish to bring this up in her presence but it has come to my attention that you are courting the Athosian."

John's interest along with everyone else's was piqued immediately, "My romantic life is of no concern to this council."

"They are if you intend to ascend her so she may join you,"

"Even if I do that is of no concern to you."

He leaned forward, "yes it is we do not wish for her to gain so much especially since you might be unable or unwilling to stop her."

John grumbled at the man, "I would do what is necessary if it came to that." He waited a few minutes letting everyone at the table fully understand what that meant before continuing. "I would like to request authorization to begin broadcasting a signal to the Wraith from Atlantis's original homeworld."

Novious smiled, he knew that the being before him disregarded most rules and had already begun doing so, a gross violation. "You have already begun doing so…"

John's eyes narrowed in annoyance, "I am still asking this council for their approval."

***

_Several Hours later_

Ganos and John remained in the meeting unfortunately for him he had been unable to slip anything interesting in the end of the meeting due to their concern over Teyla. "Would you truly stop her if she attempted to interfere in the lowers?"

His gaze was somber, "I fought The War because of interference with the lowers. I will not ever make that mistake again."

"I understand."

He smiled warmly at her, "No you don't and I'm glad you don't."

She nodded and they exited the room together.

***

"How are you enjoying my library Daniel?"

He paused for a moment to look up from his book, "I've seen a few references to a war but I don't understand its significance or anything about it."

"A war or The War?"

"The War why is there a difference?"

John sat opposite Daniel and closed his eyes remembering the entire war. "The War is the largest, longest, and most deadly war in known history. The true scope and power of those involved in the war are far beyond you comprehension but suffice it to say that it killed _Trillions._ Other factors of it would be very complicated Daniel but a war of that magnitude should never happen again and if it were to begin I would probably surrender and be destroyed myself rather than allow it to happen all over again.

Daniel simply nodded as John left.

As he roamed the hallways of his Ancient city he couldn't help but smile; His actions had set the people of Earth on the right path to assume their rightful place in the universe. It would be the research that was being conducted on Atlantis at that moment which would enable them to become what the Ancients had gotten so close to achieving.

***

"Teyla," Kanaan greeted her warmly.

She smiled and gently kissed him on the cheek, "How have you been?"

"I have missed you where have you been?"

She paused considering her answer and knowing that depending on how she answered she could be ending her relationship with Kanaan, "With John."

Kanaan's eyes flared with anger initially but quickly cooled, "Teyla I understand you have been grieving but we need to help each other through it." He paused as he began attributing another meaning to her words, "Unless you have betrayed me."

She turned on him insulted, "how could you accuse me of such a thing? I have always been faithful to you."

Kanaan ignored her, "When do you wish to undergo the bonding ceremony?"

She sighed on the one hand Kanaan was finally taking charge but on the other she didn't want to be bonded to him. "Can we discuss this after all of this has passed?"

"You mean after _John_ has left," she did not like the jealous nature of his tone or the way he spat John's name, and felt herself getting angry at him for it.

"We are very busy right now and I do not need to be preparing for the ceremony on top of that."

"Are you unprepared for it?"

She knew that once she had entered into her relationship with Kanaan that she should have been preparing for the ceremony but after they had been kidnapped she had not bothered. Before he had been kidnapped she had not taken as much interest in their relationship as she would have liked but something within her had prevented her from doing so.

Kaanan's eyes narrowed, "do you intend to bond with him?"

"John?" she forced a laugh at the notion but it sounded hollow as she considered what that would have been like.

"Yes, you have been spending long nights in his quarters."

"Do you have any idea what he is?"

"Your lover?" the accusation bit like an icy wind.

"He is the oldest of the Ancestors."

"So he claims."

"You doubt his power?"

"You have blind faith in his power?"

"No I saw him destroy a hive with ease, alter his own DNA, feed on a wraith, reverse the feeding a wraith had done on me, and negotiate face to face with other Ancestors."

"I have seen none of that."

"You don't trust me?"

"When it comes to _him,no_."

She felt something in her mind, _"You can trust John but can you trust Kanaan? The man who refused to help you."_

"_Who?" _She was momentarily confused the only one who had communicated with her like that was the ships AI,_ "Oh Lanti. Where is John?"_

"_His private lab."_

"Teyla I need you to show at least some commitment."

"_Kanaan _I was _pregnant _how much more committed can I get?"

"You did not have the child."

"It was not my choice," Teyla worked to reign in her emotions. John was slowly starting to allow her to grieve for her lost son. "_Is John busy?"_

"_No."_

Kanaan noted the change in Teyla's posture and correctly surmised that she was about to leave, "Can we discuss this over dinner?"

"I will call you later."

***

Teyla was heading towards John's lab when Ganos materialized beside her.

"I wish to speak with John."

"Why?"

"You say he is the same as before? He is my friend."

"How is Kanaan?"

"Well."

Ganos pursed her lips and shook her head unhappy with the situation. She knew that she couldn't actually prevent Teyla from seeing John, but she could delay her. "What are your intentions with John?"

"That is not a matter of your concern."

"Yes it is."

Teyla was becoming impatient with Morgan's stalling, "allow me to speak to John."

Morgan shook her head but backed away.

She passed Morgan and entered the darkened lab, "John?"

"Yes," he called coldly from deeper in the lab.

She slowly moved towards him wary of his anger and the dangers of walking in a pitch black lab. "How was your meeting?"

"Not well."

"Why?"

"The nosy bastard went too far." He slammed something metal onto the desk causing her to jump back.

Teyla realized why Morgan didn't want her to enter, John was clearly upset and she was in way over her head. She couldn't debate ancient politics with John, "Is it anything I can help you with?"

John turned around and looked at her, "no I'm sorry for that. What's bothering you?"

"Morgan has indicated that you have feelings for me."

"She's right."

"John, how could we really have a relationship?"

He sighed, "It would not be easy, you could join me or I could visit you."

"Join you?"

"Yes ascend to my plane, however I must warn you that would be a permanent change and one not taken without serious consideration."

She nodded, "what did the ancients want?"

He managed to control his anger and prevent it from entering his voice, "they inquired into our relationship."

"Ah."

Lanti appeared on John's desk, "the wraith will be in position in two days."

John nodded and she disappeared. "I will leave you to your work."

"I'm done."

"I…I…"

"You don't have to stay if you don't want to."

"I…I'd like to stay."

"One second."

Lanti appeared again, "what is it John?"

"Postpone tomorrow's meeting until after the wraith will have been defeated."

She disappeared again, "John what was your childhood like?"

***

"Carter, Jack we're going to be jumping in two days."

"Where to?"

"My original homeworld." Lanti answered.

"Why?"

"Lots of wraith there and I want to go home."

"Sounds dangerous."

"Not really and the wraith need to be destroyed."

End Chapter 27


	28. Chapter 28

Start Chapter 28

"John, I have to go," Teyla said sadly.

"Ok, you know where to find me."

***

Teyla entered Kanaan's quarters, "Kanaan how are you?"

"I am well Teyla although I have missed you. How have you been?"

His words were kind and she happily smiled, "I am well."

"Come I have made us dinner."

She looked at him uneasily he was being far too nice and formal, "thank you."

Teyla sat down opposite Kanaan. She stared at her food lost in her thoughts. "Teyla where were you today?"

"What? Oh I was with John."

"John?"

She winced, she sensed that Kanaan had a problem with John and he was unlikely to get over it any time soon. "Yes John, do you have a problem with that?"

"Yes, I do not like how much time you have been spending with him."

"He is my friend."

"And lover?"

"Kanaan I have not been unfaithful to you."

"Teyla I do not think I can trust you with him."

"You cannot control every aspect of my life."

"Teyla it's me or him."

She stopped unsure of how to respond. She closed her eyes, lowered her head, took a deep breath. Her voice was low barely above a whisper, "John." She got up and left his quarters heading back to her own.

She stayed there for a few hours crying for her son, Kanaan, John, and herself. Eventually however she knew she had to get up and do something. She wandered mindlessly through the city hoping to collect her thoughts.

***

She found herself at the door to John's quarters. She palmed it open. She activated her radio and sent a quick message to John, "John can you come to your quarters please." She waited a few minutes and heard him open the doors himself. She was shrouded in darkness, but he was illuminated by the light from the hallway, it was enough for her to notice how nervous he looked. He stood in the doorway unsure of what to do. "Teyla?"

"In here."

He stepped into the room searching for her; seeing him so nervous and human injected her with a dose of confidence and she closed the gap between them standing mere inches from him, "did you mean it?"

"Uh…mean what?" He was unnerved by how quickly she had gotten close to him.

"What you said on the Wraith hive." She looked up at him hope filling her eyes.

He smiled to her, "Teyla, I love you."

Her heart soared; she had longed to hear him repeat those words since she'd gotten off the Wraith hive. "John, I want….I want you."

She pulled him down into a heated kiss. She smiled against his lips as she maneuvered them towards the bed. When he sensed what she was doing he pulled back, "Tey I don't think you...it's." He knew that she didn't fully understand what this would mean for him.

She smiled for a second at him calling her Tey before she was lost again in the feel of him against her, "shhhh, I-we both want this."

Her hands had already found their way underneath his shirt and she pushed him down onto the bed with her. As he hit the mattress he realized he didn't care if she understood the importance of it; he loved her and he didn't want to be with anyone else.

***

She woke wrapped in his arms, smiling. She snuggled closer to him turning over and stealing a good morning kiss from him.

He had awoken a few minutes prior and quietly enjoyed the feel of the sleeping woman in his bed. When she awoke and snuggled closer to him he was slightly reminded of the last time she had done something like that. Another lifetime ago back on the ship. He knew what that night meant even if Teyla didn't. "Good morning beautiful."

She smiled at him a wondrous glorious smile, "I think I'm rather fond of waking up this way."

"So am I, I want to stay but Rodney wanted me to help explain some things."

"You're going to leave me for _Rodney?_"

"Do you have any reason I should stay?"

"I think I can think of one or two."

***

Teyla whimpered beside him as he slipped out of her grasp and planted his feet on the floor. "I'm sorry Tey but I really do have to go."

She smiled sadly at him, "I guess I'll just have to entertain myself than," she crossed her arms and pretended to pout.

"He turned back to her, "hey I'll come back as soon as I can."

"Perhaps I should show you what you'll be missing," she said as she planted light kisses on his back as he sat there searching for his discarded clothes.

"No really I need to go."

"Stay."

"Teyla, if you ask me that one more time I'm liable to say yes."

"Please stay," she smiled at him.

"Tey."

She smiled at him until he opened the door.

"John are you really going to leave me here and go see _Rodney_?"

"I wish I didn't have to," He said sadly. He turned and smiled at her, "I love you."

He left before she was able to respond.

She watched the door close behind him. She turned over and closed her eyes hoping to catch another few hours of much needed sleep. A few minutes later the door opened again admitting Morgan. Her entrance startled Teyla who instinctively covered herself in John's sheets. "Hello Teyla."

Teyla smiled uncomfortably, "Hello Morgan, can I ask why you are here?"

"I was looking for John," Morgan lied.

"He is with Rodney."

Morgan glanced around uncomfortably, "Teyla, if you don't mind me asking, did you and John…have… sex?" She looked mortified at the idea.

Teyla smiled, "yes, I chose what I wanted and took it."

Morgan's eyes went wide, "do you have any idea what you just did!"

"Besides John?" The Athosian laughed she felt free and happy for the first time in a long time.

Morgan's eyes flashed with anger, "now is not the time for fun and games."

"What's the matter we're both adults, I thought about my decision and I want John."

"Teyla did John explain his mating rituals?"

"With words? No we were kind of preoccupied."

"Teyla, you don't understand John mates for life."

Teyla paused for a moment, "so John will not be with anyone else besides myself for my life?"

"No, for his."

"His life?"

"Yes."

"And if I die?"

"He won't mate again."

Teyla laid there stunned into silence. After a few minutes and many attempts she finally managed to choke out a two words, "how-why?"

"You're aware that John and his species weren't the result of evolution, but of genetic manipulation and design?"

"Yes."

"Well when the original three were constructed they eventually noticed that the third one was rather promiscuous and they worried that he had a looser moral and ethical code than they would have liked. Considering their power their creators correctly felt that a strong moral and ethical code was necessary. When they created John they did everything in their power to ensure that he would have a strong moral code."

"They succeeded I take it?"

"For the most part."

"What about the first two?"

"They ended up becoming each other's mates."

Teyla felt sick and betrayed at the thought of what she had just done to John, he would never mate with someone else again. She knew she would feel compelled to join him permanently so that he would not be alone for eternity. "How did they?"

"Make him that way? I don't know and he's never helped us get anywhere near that level of advancement. How advanced his creators truly were is unknown as he refuses to discuss them."

"Why?"

"It is painful for him and he does not wish to give away everything they could do."

"If John didn't want to alter your development why reveal himself at all?"

"His beliefs are complicated, but the primary reason was because did want to help us but not to the point where we would be achieving their level of technology."

"He said he wanted to help Earth and the rest of humanity with its technological development."

"He will help you get to our level but not anywhere beyond that."

"Morgan, John offered to help me ascend and join him."

"That would be a major undertaking one and I would suggest you think long and hard about it as once you go down that road there is no turning back. Be aware also that the council does not look kindly upon that prospect and would do everything they could to deter John from that course of action."

Teyla nodded. "Am I interrupting something?" John asked as he walked in on the two.

"No I was just leaving, and I imagine you and Teyla have other matters to attend to."

Teyla turned towards John and he felt her anger radiate out towards him, "you should have told me."

John detected the anger in her voice, "Teyla what's wrong?"

Her anger peaked, "YOU SHOULD HAVE TOLD ME."

John backed up and raised his hands in a defensive posture, "told you what?"

Her eyes were ice, "that you mate for LIFE."

"I did not think it would matter."

"Doesn't matter? John you just committed yourself to me for eternity and I've never even told you that I wanted anything more than sex."

"Do you?"

"That is not the point." She knew that truthfully she did want more, much more.

"I think it is."

"John you just chose me without even considering that this might not work out. What would you do if I died or left you?"

"Would you?"

"John!"

Teyla, I love you there's no one else I'd rather be with."

She shook her head, "John how could you be so rash?"

"I tried to tell you, but I got lost after you kissed me."

She tried to be angry with him, but felt her will breaking under his touch and gaze. "John."

He took another step closer to her, "I can't say I'm sorry."

"Do you understand the position you put me in?"

"What position?"

"Force you to be alone for eternity or give up my life."

"I'm sorry I didn't mean to put you in that position.

She finally felt the last ounce of anger evaporate as his lips gently brushed against hers. She smiled, leaning into him and deepening it. As her tongue fought with John's she was reminded of their sparring sessions, she felt a momentary desire to engage him in one. That thought however was quickly discarded as she felt the passion within him. "No, John we need to-"

"-Damage is already done."

***

She drew lazy circles on his bicep while he dozed peacefully next to her. She felt him slowly begin to stir beneath her touch, "John we really need to talk about this."

He nodded knowing it was inevitable, "Teyla, I trust you. I love you. I'm not going to wait around and see if anyone better comes along, that's not what I want."

"John I…I don't want to hurt you-"

"But you can't say yes."

"No."

"I understand, I'll be leaving in a few days."

"I'll miss you."

"Tey, you just have to say my name, I'll never leave you alone for long."

"I…I…John I-"

He placed his finger on her lips silencing her, "I never needed the words."

End Chapter 28


	29. Chapter 29

Start Chapter 29

"Coming out of hyper-space now."

Atlantis's re-entered normal space to find itself near absolutely nothing but a single ship. A few scientists recognized it as the first of their latest assortment of toys, "Sheppard what's that ship doing here?"

"It's my ship Rodney."

John tapped a button initiating a comm. link between Atlantis and the ship, "Virgil report your status."

"Virgil?" Rodney asked.

"AI's name."

"I thought he was named Ancient?"

"No, that's what the ancients call him because they call me Ancient and he's my ship/AI."

Virgil appeared nearby on a console, "The wraith have all received the message and should be here within a few hours."

Lanti appeared on John's shoulder, "Virgil it's good to see you again."

"Et tu, I was worried about you when I was on the planet; I was unable to sense you and the ZPM was active."

"John," Teyla entered the room quietly interrupting the talking computers.

"I sense the Wraith approaching."

Virgil chimed in quickly, "Considering the amount of Wraith converging on this location she would be able to sense them from a much farther range than normal.

"Teyla, if you would like I can shield your mind from the Wraith."

Morgan materialized behind him, "Ancient." She warned simply.

"I will not harm her or take anything merely build up the walls protecting her from intrusion."

"That's what I'm afraid of, you will take away the pain you find there for her son and she can barely feel it as it is now."

"Morgan it is ok, John please do the Wraith in these numbers may threaten to control me."

"Teyla are you coming to the meeting?"

"John the Wraith are almost here!"

"Lanti will handle them besides the initial communication." He paused for a moment, "It's going to be an amazing show here perhaps you should stay out and watch it."

She nodded, "Morgan?"

"The Wraith have tortured your people for millennia I think it is only fitting you witness their downfall and extinction."

"Every Wraith will be here?"

"No, I will be destroying any that are not here via, Ancient and my own abilities."

"I would like to stay outside if it would be acceptable."

"Of course, but I must go now."

They disappeared into the meeting room.

***

"_Colonel Sheppard the Wraith are entering in system."_

"Excuse me for a moment I have to send a message." John stepped out as the Wraith ships exited hyper-space surrounding the city.

John emerged in his usual Atlantis attire, "receiving a message from the Wraith armada."

John stood before the screen as a wraith queen appeared on it. Teyla, Carter, and anyone else around gathered around behind him. "Surrender our quarry now," the queen hissed.

"I don't know what you are talking about."

"Our prey, the immortal, will be given to us NOW." She repeated angrily.

Teyla stepped up next to him and placed her hand on his shoulder, "John, are they talking about Ancient?"

"Yes, they are Tey but we're not handing over anyone." He brushed his hand over her cheek.

"YOU WILL DO AS I COMMAND OR BE DESTROYED."

John laughed, "I don't think so."

"The Ancients could not resist a bombardment of this size so what makes you think _you _can?"

John smiled, "remember what happened to the final fleet that seized Atlantis?"

"They searched for food elsewhere."

"No they were totally and utterly destroyed."

"LIES."

"No, I was there, I'm the one who did it."

"Impossible." Despite the proclamation the queen still showed some fear.

"I'm giving you one last chance, stand down or be destroyed."

The Wraith laughed, "if you will not hand him over we will destroy you and your whore," she spat motioning towards Teyla.

She heard John utter a primeval growl, and his eyes blazed with anger as he cut the comm. channel.

Teyla intertwined her hand with his and placed her other hand on his shoulder hoping to calm him, "Sir, we are getting another message from a different hive."

The screen flared to life again with a familiar male wraith this time.

"Sheppard."

John worked to control his anger, "hello Todd."

"Turn over the immortal it is your only chance to even have a shot at living."

"No Todd this is your only chance to survive either take the retrovirus or be destroyed."

"You are in no position to negotiate with me."

"On the contrary, I as the one contributed to the rise of your species am in every position to negotiate your _surrender_. Your kind have killed far too many humans to be allowed to survive."

"You…You…You are…the immortal?" His entire body showed defeat, he knew his species was dead and accepted his own fate.

The Wraith fleet opened fire minus Todd's ship which joined in a minute later. Todd cut the comm. link leaving them to stare at a blank screen the image of his blank stare convening the enormity of the situation he found himself in, and while he knew he wouldn't win he had to join his species and fight.

"Make it a quick death for him."

"And the rest?"

"Let them suffer."

John stared out a window as an energy beam erupted from one of Atlantis's piers; it impacted Todd's ship instantly killing everyone on board. He shook his head, knowing that he would once again be forced to commit genocide.

"John, you had no choice."

"I always have a choice; I just chose what's best for the future."

He disappeared back into the conference room as Lanti opened up the rest Atlantis's weapons systems.

_She smiled as she felt the city's firepower being brought to bear fully for the first time under her control. She felt her drones cutting into the Wraith cruisers smashing through bulkheads and detonating in the center of the ships. She felt the directed energy weapons charging and discharging throughout the city as they precisely cut through Wraith ships. She felt the plasma discharges as they boiled through the space engulfing darts that were to slow to get out of the way and then impacted both hives and cruisers superheating their hulls and boiling their way towards the center of the ship. She controlled the anti-matter weapons as they fired their engines and rocketed towards Wraith ships; they impacted enemy ships causing the destabilization of their containment chambers and the release of the anti-matter. She controlled Ancient fighters and bombers as they engaged the darts in combat, pulling maneuvers that would kill any human or Wraith. She controlled the shields as they shrugged off the massive bombardment and simply drew more power from their near infinite energy source. She looked into some of John's more potent weapons systems but disregarded them as overkill. She prepared a singularity, for the cleanup._

She was shaken out of her reverie by an innocuous question, "Lanti what is happening over there?"

She shook her head and directed her attention to the people in her control room.

Teyla was pointing towards an area near the base of the tower where a purple hyper-space window was located. "Those are drones being sent into hyper-space and will emerge just in front of the Wraith ships, because they lack any way of decelerating they will punch through the hull of the wraith ships and continue on through until they reach well inside the ships where they detonate causing significant damage."

Teyla returned to staring at the mesmerizing light show of weaponry crisscrossing the sky. The Wraith's weapons dissipated harmlessly on the shield while their fleet took heavy losses. The battle was horribly lopsided in favor of the lanteans and within a few minutes the wraith ships were turning to open hyper-space windows. "Oh no you don't."

She smiled as she activated a jamming field preventing hyper-space windows from forming.

***

They emerged from the conference room to find the control room mostly empty of personnel with a few watching the final hours of the light show. "Lanti report."

"Wraith ships destroyed, Virgil has a few left to destroy although I assume you might want to handle a few of them personally, I couldn't get the Wraith queen off the Hive though she self destructed her Hive before I could take out the jammers."

"No problem, they Ancients won't mind if I take out some vengeance on her."

"Resurrection? You haven't done that in my lifetime."

"I don't use it often but I think she earned her punishment."

"She did insult your mate."

"What are you doing now?"

"Cleaning up," she was using her plasma weapons to burn the wrecks of the Wraith ships into small molten cores.

"Tell Virgil, I'm taking out the rest of the Wraith but when you're finished here land."

John smiled as he walked out onto the balcony slowly allowing his body to take upon a fully ascended form. As he reached it he saw and felt the universe like no other, he sensed each bit in the universe and in a single moment of revenge tore each Wraith, and each Wraith ship apart. In one moment he eliminated the Wraith species.

***

"It's done."

"We should be home in a few hours."

"Where's Teyla?"

"Your quarters, but Ganos wanted to speak to you."

"Where is she?"

"Right here."

Morgan moved out to the balcony John was standing on, "what's the matter?"

"What were you thinking?"

"About what?"

"Teyla."

"I made my decision."

"She hasn't."

"Morgan, I'm sorry you disagree with my actions but I don't regret them."

"I hope you never do."

"They've returned to Earth to inform the IOA of the situation."

She offered her hand, "Well congratulations you managed to get most of your measures passed."

"Thank you, so did you although I'm sorry I couldn't help you keep your normal seat."

"I'll get it back in the next election when people realize mediation and compromise are the best ways to temper your ambitions and actions rather than going to an extreme and refusing to compromise."

"Good, you're right to."

"I'll say goodbye to Teyla tomorrow if it's ok with you, I'd like to walk amongst the city tonight."

"Go ahead."

***

John eagerly opened the doors to his quarters. He had been anticipating seeing Teyla again since Lanti had told him she was waiting in her quarters. "Tey you up?"

"John, you certainly took your time."

He just smiled at her as an answer. She returned his smile as his lips crashed onto hers.

***

She looked at the rising sun, "I should go."

"Why?"

"Kanaan, I must tell him that we're pursuing a relationship."

"He's not going to take it well."

"No he won't."

"Want me to be there?"

"No, I don't think he'd appreciate both us telling him."

"I'll be in the control room if you need me."

***

Teyla moved quickly through the halls knowing Kanaan liked to sleep in late. She arrived at his door a few minutes later. She waved her hand over the chimes and waited for him to admit her. "Hello Teyla," he greeted calmly stepping to the side to allow her in. "How have you been?"

"Well and you?"

"I've missed you."

"Kanaan we need to talk."

"You wish to discuss the bonding ceremony?"

"No, I…Me…We're over."

"What?"

"We're over, I am pursuing a relationship with John now."

"WHAT?"

"Kanaan I'm sorry I never should have started our relationship."

"SO WHAT THIS WHOLE TIME I'VE BEEN WHAT? SOMEONE TO DATE TO PASS THE TIME?"

"No."

"YOU'RE LEAVING ME FOR AN OUTSIDER HE'S NOT ATHOSIAN TEYLA."

"I…I…I love him."

"HE'S NOT EVEN FROM THIS GALAXY."

Her self-restraint snapped, "YOU DO NOT KNOW JOHN."

"I KNOW HIM WELL ENOUGH, HE IS LYING."

"JOHN WOULD NEVER DO SUCH A THING."

"YOU'VE CHEATED ON ME HAVEN'T YOU?"

"What? I…I, I'm sorry."

"You…You little…I'm leaving."

"What?"

"I do not wish to be in a society where _you _are the leader." Kanaan stormed out.

"KANAAN WAIT." She screamed after him already in pursuit.

He stormed off to the nearest teleporter. Teyla followed him and managed to get in before he teleported away. He ignored her the entire time she had been following him and didn't react to her getting into the teleporter besides tapping the button with a disapproving sigh. They emerged from the teleporter onto the gate room. "Kanaan talk to me."

"Dial the gate."

"What? No, Kanaan don't leave like this."

"Teyla you've betrayed me, it's either me or him," he gestured to John who was emerging from Carter's office.

"What's going on here?"

"Dial the gate."

John stared at him confused for a moment, "Is that what you really want?"

"DIAL THE GATE."

"Lanti make sure you don't dial a space gate." He was serious, he wasn't killing Kanaan like that.

Kanaan's eyes slid over to John hate filling them, "You'll pay for this." He hit the gate technician and grabbed his side arm. He first pointed it at John and fired two rounds, then he aimed it at Teyla. As soon as it got close to her it flew out of his hand.

"Run and hide, Kanaan, run and hide."

End Chapter 29


	30. Chapter 30

Start Epilogue Part 1

A/N Most European cities have a New version in the Americas New York while the most famous isn't the only one. I didn't make a mistake there.

"Rodney, how was Earth?" Teyla asked as he stepped through the gate.

"Good, New New York, New New London, and New New Paris are almost done, the rest should be done by next month."

"Parliament?"

"Completed and submerged."

"So you were able to successfully build ZPMs?"

"Yeah, how's Ronon?"

"He is bored, he misses the old days." She sighed, she was bored to.

"Well I imagine he doesn't have much to do considering he's the military commander of a peaceful galaxy. How are you?"

"I am well, although I must admit I find some of our practices disconcerting."

"Like what?"

"We basically force planets to join us or we destroy them."

"They haven't updated that yet?"

"What do you mean?"

"They're supposed to make it so that we would just isolate the planet not destroy it, more in line with our charter that way."

"Yes, well I have seen several planets attacked and even one glassed because they refused to join."

"Wait they glassed a planet?" Rodney was surprisingly angry.

"Yes," she said sadly.

"Did they have a reason?"

"They killed the delegation sent to the planet."

He nodded in understanding, there had been a huge uproar when they had been killed. "Oh that planet, they glassed it?"

"Yes Rodney that's what I've been telling you."

"That planet was filled with a bunch of pirates and scoundrels."

"That does not excuse your actions."

"Rogue Genii had sold them a nuclear weapon."

"What did we do to the Genii?"

"They're alive probably on P3X-2479."

"That is the ice planet with the space gate?"

"Yeah the prison planet."

"Have you seen John?" Rodney asked as they headed out onto the balcony.

She blushed slightly as she remembered the last time she had seen him, "yes a few times."

"Do you know what he thought about us?"

"We did not spend much time discussing politics."

"Oh, are you ever going to come to Earth? We'd love for you to meet the twins." Katie had given birth the month before.

"I am very busy Rodney, but I'll try and visit soon."

"Ok, how's the integration of the planets going?"

"With a few exceptions very well, Athos has taken a lead role."

"How are your people?"

"Well, they are trading again and our first city is set to be completed at the end of the quarter."

"You're doing finance reports?"

She smiled, "yes as I said I'm very busy."

"Atlantis is still as beautiful as ever."

"Lanti tries."

"She still around?"

"Oh yes she was very excited last month when you said you'd managed to create your own AI."

"Lanti I've got it on me if you want to install it."

She appeared smiling at him, "thank you."

***

John smiled at her as she prepared to head to Earth for the first time. "Tey you sure you don't want me to stay? Or come with you?"

She pulled her top on, "I think you'd be recognized pretty quickly and we both know they'd have a billion questions for you."

"We could just stay in the hotel."

"I have to give my report and Rodney and Katie have invited me to spend time with them."

"Well if you ever get lonely just call me."

"How's Morgan?"

"Good, she should win her seat back next month and the Ancients have finally completed their information superhighway."

"Good, how have you been?"

"Fine, it gets a bit boring and lonely up there though."

He pulled her down into a kiss, "No, John we had all night together and I've really have to go."

He smiled at her.

"I have to go, they need me to give a report on the progress in Pegasus."

"Stay here and give me the report."

"John," she said as she pulled on her coat and headed to the door.

"You going to be here when I get back?"

"Maybe."

She walked out smiling at him.

***

Teyla flipped through the contents of her folder, "it's been almost two years since your program was started."

"Yes."

"Ms. Emmagan how has it fared?"

"Sheppard."

"Excuse me?"

"Call me Mrs. Sheppard."

"I'm sorry I was unaware you were married."

She ignored her apology, "The program has been very successful we have three planets which should be able to rival Earth within the decade and most of the others will be on track to become productive members."

"That seems a little sluggish only 3 planets on track to becoming equal to Earth."

"How has the Milky Way fared?"

"All planets are on target to meet production goals with 5 approaching Earth level capabilities within a decade."

"Do those numbers include the Jaffa worlds?"

"Yes."

"Those Jaffa planets have had years to create working advanced societies we've only been without the Wraith for a little over two years."

"Perhaps but I think you could have done more to achieve your quotas."

"I exceeded my quotas."

"Oh."

"Anything else?"

"Yes, what is your relationship with John Sheppard?"

"What do you mean?"

"Do you see him often? I assume you took his last name?"

"I see him from time to time, and is it not a custom among your people to take the last name of one's husband?"

The bureaucrat nodded, "what does he say about us?" Another asked earnestly.

"We usually do not speak of politics."

"But you do rarely?"

"We have spoken of them."

"What did he think of us? Did he say we were doing a good job?"

Teyla sighed some people here had a near god like reverence for John. Her steely gaze fixed on the weak bureaucrat, "When I am with John we generally discuss my efforts in politics such as the progress of Pegasus. We do not spend our time debating tax policy and trade negotiation progress. There are also other things that we prefer to do together."

"Such as?" the same politician asked.

"Who was the idiot who put Mr. Alnip on this committee?" A formerly silent politician asked. "Are you really so stupid that you're going to ask Teyla what her and her husband do during their alone time?"

"What? Well I just-"

"Just what? Wanted to get some good stories to tell your drinking friends? You might have a brain for numbers but that won't keep you safe forever."

"Hey he's earned his position, he was duly elected by the people."

"The people of what planet? Oh that's right P7C-9126 a SCIENCE planet where everyone else is too busy to run for office."

"I was duly elected by the people."

"Oh shut it, I'm not going to have you removed from office just take your seat and learn your place."

He glared at Teyla's protector but closed his mouth and simply sat staring at her for the remainder of the meeting.

"Teyla, thank you for your time and in the future if you could possibly ask John what he thinks of us; he does have an official position and if he wanted to appear in it more often that would be fine with us."

Teyla smiled, "you really wish to know what he thinks of you."

"Of all of our policies not me specifically."

"Ok, John."

The committee stared at her perplexed.

"Wait a minute."

Teyla was vindicated a moment later when the council door was opened contrary to procedure, the chamber was sealed while in session. John walked through calmly wearing a self satisfying smile, "how are you today my love?"

"Well John."

"What's up?"

"They are curious about your opinion on their government."

John rolled his eyes, "you are doing fine perhaps be a little more understanding of planets that don't want to join you but your current policies are within the range."

"It is an honour to meet you."

"Thank you, good luck with the ruling."

"Wait, we would like to go over several other matters."

"Teyla…"

"Goodbye John."

"Sorry."

Teyla turned back to them hoping their curiosity was satisfied for the moment. "Anything else?"

"There will be a party to celebrate our new treaty with the Jaffa in two days and we would like you to attend."

"Send the invitation to my hotel room."

***

"You look great," Ronon said as she turned around in the mirror.

"I do not share your optimism," Teyla frowned at her appearance in the mirror.

"John gonna be there?"

"Perhaps."

Ronon shot her a knowing look, "Why haven't you accepted his offer yet?"

"I have things to do. You should get ready."

Ronon shrugged, "figured I'd just go like this."

"You are going to an Earth dinner party."

"I don't have any suits."

"Woolsey had me pick up a tuxedo while I was on Earth."

Ronon stared at her as she handed him the tuxedo, "I don't care what you make me put on I'm not going to fit in."

"Take it up with Mr. Woolsey."

Ronon retreated from her quarters. "Lanti."

"Yes, Teyla."

"Give me a status report on Larphtia."

"Negotiations are proceeding although their progress has slowed current projections put them joining in 2 weeks or declining in 3 days."

"Update me with the new projections after the days conclude."

"They've returned to their planet for day to consult with their leaders."

"If they return message me regardless of where I am."

Teyla headed down to her personal control room where all of her work was located. "Any other updates?"

"Rodney's AI is finally coming out of its shell, there have been a few new medical advances today, the markets are up again, and Lorne will be commanding a strike team to root out a rogue genii base."

"How are Rodney's R&D projects going?"

"For reverse engineering my weapons systems nowhere; for his normal projects they're proceeding along normally."

"Thank you."

"Teyla Earth has enacted some new protocols for tonight so please don't wait until the last minute. Remember the people there are going to be trying to kill their opponents and some might have friends who want your job."

"They can have it."

"Teyla…"

"Lanti I've been in politics my entire life but this time I've got a secret weapon."

"John."

"I bring him up and they'll be so distracted they'll forget I even exist."

Lanti nodded and disappeared.

**Mission to Sivos**

"Please come this way our king has graciously decided to grant you an audience," one of his numerous attendants called from an upper balcony out into the courtyard where Teyla and her negotiating team waited. Teyla packed up her bags and headed inside with Ronon's men guarding her and her team she didn't even bother carrying a P90 with her anymore just a simple sidearm on first contact missions.

"Teyla I know you have experience with this kind of stuff and all but do you think I can take the lead in these negotiations?"

Teyla nodded tiredly she was beat after days of negotiating with another planet that had been adamant about maintaining some of their antiquated ceremonies. She had personally wanted to lock the planet out after first discovering that they liked to sacrifice people to the Ancients.

They walked through a series of chambers that were lined with guards armed with swords and spears. As they proceeded deeper the spears and swords were gradually replaced with guns that were obviously there for more than simple show. They finally came to a grand door that was several meters high; it parted for them as the ascended the staircase leading up to it. Once inside the grandiose chamber Teyla was awed by the vast display of wealth and power. The king's court was filled with elaborate tapestries, numerous dancers, soldiers dressed in intricate uniforms, and numerous gold plated objects ranging from chairs to cups. The throne appeared to be made out of gold and then gemstones were implanted into it in a swirling formation.

"Good you have-my, my you're quite an exquisite gift," Teyla looked at the king who was sitting next to his wife. She was immediately put on guard as the king advanced on her ignoring his queen. The queen didn't even seem to notice that her husband was ogling another woman only yards away from her. Teyla immediately took pity on the woman who was trapped in a marriage to a man who Teyla had already developed a distaste for.

"King John it is an honor to meet you. I'm Henry lead negotiator for this team."

"Yes I'm sure you're wonderful, but who is this beauty?" The king said staring rather inappropriately at Teyla.

Teyla rolled her eyes, "I am Teyla Emmagan minister of interplanetary relations for the UHR." She used her maiden last name for trading in Pegasus as many people knew of the Athosians and her father but few knew of her relationship with John or what John really was.

"UER?"

"United Earth Republic," her protégé answered attempting to retake the lead on the negotiations.

"Hmmm and have you come to join my royal court?" He grinned lecherously at Teyla.

"No, I have come to observe my protégé during his first lead on a first contact mission."

"Perhaps you will stay though?" He eyes still hadn't made their way above her neck.

She rolled her eyes already tired of dealing with him, "No."

"I think you will."

"I won't."

"You would make a wonderful addition to my harem," She was becoming angry with the king.

"I will not be staying with you."

The king turned back towards Henry, "perhaps we can negotiate for her?"

"No."

"It is the only thing you have that is of value to me."

"We have technology and resources that would greatly aid your civilization."

"I want her and only her."

Teyla was seething, she would have loved to see this man's kingdom burn, but she knew that would be unfair to the thousands of innocents who would be killed. "Look we don't trade our people away and if you're even thinking about kidnapping her you should know that we stop at nothing to get our people back." Teyla smiled at her protégé's protectiveness.

"You have nothing else to offer me besides your women," the king flashed her a smile that made her feel nauseous. She realized that this would not end well this guy would not be willing to give her up.

"Then we're leaving." He said.

"You can. She's not."

Ronon's men immediately brought up their weapons and moved to cover her and her team.

"Lower your weapons no one needs to be harmed here the rest of you are free to go apart from Teyla, and you," he pointed to the only female marine. They kept their weapons up eying their targets anxiously.

"Lower your weapons I am sure we can work out some sort of deal," Teyla calmly told the soldiers.

"Ma'am are you sure?"

"Yes captain I believe we will be safe."

He shook his head but complied with her request, "happy now?"

The king smiled at the soldiers who were obviously unhappy about being forced to surrender.

"You should know my mate will not be pleased with your actions."

"You are bonded?"

"Yes."

"No matter I am sure he can find another."

Teyla remained silent her eyes giving him a last chance to save himself.

"What is his name?"

She smiled, "John, John Sheppard."

"His deeds are well known although I heard he disappeared perhaps I can give you some much needed companionship."

"Oh he hasn't disappeared in fact he should be here shortly."

"No one can get past my guards without my authorization."

John chose that moment to make his entrance. Two guards exploded through the giant doors and a solitary figure ascended the steps up to his court. She recognized him immediately, "last chance."

"I…What is the meaning of this?"

Teyla shook her head, it was too late.

"You have attempted to kidnap, forcibly marry, and then rape my mate I suggest you don't speak and perhaps I'll simply kill you."

"GUARDS." More guards streamed from behind his throne out into the room and aimed their weapons at John.

He flicked his wrist at them in a dismissive fashion and the weapons disappeared, "fools." He calmly strode from one end of the hall to the other as one of the guards charged him. The guard attempted to punch John but was proved far to slow as John dodged the punch grabbed his arm, broke it, spun him around, twisted his arm behind his back, knocked him down, and broke his neck in one a matter of seconds. The king looked horrified at John's display of physical prowess and unsympathetic nature.

He glanced around the chamber at the horde of guards, "I suggest you don't try that again."

They took a collective step back leaving their king to fend for himself. John approached the Lantean group and smiled, "I already notified Atlantis they're sending an extraction team to pick you up they should be here within the hour."

They stared awestruck at him. "Thank you, sir," one of John's old soldiers said for the rest of them.

"Hello John."

"How are you Teyla?"

"Thank you for coming," while she would have liked to have avoided bothering him she was still angry at herself for how she had behaved at the party and wanted to take every opportunity to thank John.

"Thanks for not waiting so long." He walked over to her wanting to kiss her for the first time since the party.

"I won't make that mistake again." She smiled as they shared their first kiss in months.

As it ended he turned to the king, "and now you."

"Well since she is in fact already bonded she is free to go."

"No."

"I can have her?" The king was shocked he'd never had the leader of another world offer his mate to him.

"No, you're not going to have anyone ever again."

"I apologize for my actions towards your mate I didn't know."

"Your actions are inexcusable and your very existence offends me," John's eyes were now a cool orange color purposely changed to reflect his temper.

"Surely we can work out some sort of arrangement…"

"Are you next in line to the throne?" John asked looking the Queen who appeared to be amused by the situation.

"Well technically although my son will become the next king when he becomes of age."

John looked back at the king, "looks like your obsolete."

"What? I-No you can't do this to me-"

Teyla stepped up placing a calming hand on John's shoulder, "let me do this…please." She whispered in his ear.

"Are you sure?"

"Yes."

John nodded but didn't move from his spot.

"I find you in violation of UHR law and you will now be escorted back to Atlantis to stand trial for your crimes."

"Wait." His wife called from her throne, "allow me to at least have one last goodbye."

She walked over to his throne and grabbed something before heading over to the king.

John and Teyla walked away confident that King John wouldn't try and escape. His wife walked up to him and revealed what she had taken from his throne. His favorite pistol. "Thank you Linara once the leader is dead the rest will surrender to me," He whispered to her.

"This isn't for you, it's for me." She raised her weapon aiming it at his head and pulled the trigger getting the revenge she had so richly wanted since she had first caught her eyes as a teenager and been forced to marry him.

John and Teyla spun around shocked by the gunshot and the military escort raised their weapons at her preparing to fire should she seem the threaten any of their people.

"Bastard." She tossed the gun away reassuring everyone that she was simply going to kill him.

"You could have let us take him."

"You saw what he was going to do to you, he's been doing that to me for years."

"Please you may return home we have much to do the tyrant has ruled over this world for many, many years and we must adjust to life without him."

Henry spoke up, "We'd still like you to join."

"Come back another month to renegotiate."

"Thank you," he extended his hand.

She shook his hand, "please you may wait outside for your people."

"Thank you and good luck." They moved quickly towards the exit.

***

The jumpers had arrived about half an hour later and the team was now boarding.

"Goodbye John, it was good to see you again."

"Goodbye Teyla." John gave her a quick goodbye kiss before she boarded the jumper and then disappeared back to his normal realm.

***

Teyla stood in her quarters dressed in the same clothes she had been wearing years previously when she and John had first met. She stood next to the table in John's quarters finishing a note which she than left open on the table. With that finished she picked up the pistol off the table and closely inspected it.

End Epilogue Part I


	31. Chapter 31

Epilogue Part 2

She walked through the gate with the other ambassadors smiling something which in recent months had become a rare thing for her. She wasn't unhappy with her job but she knew so much more was being offered to her and all she had to do was say yes to him. Her father had happily become the leader of the Athosians again and no one had heard anything from or about Kanaan since he had left Atlantis so she really had no reason to delay and yet she had done so for months. The other members of her delegation were grumbling about the lack of a Jumper and the walk to and from the gate one of the Ambassadors complained so much that he reminded her of Rodney and his whining. As she looked around the planet she was reminded of Ronon, he had asked her not to go and she had considered agreeing when she felt John's presence she assumed he also wanted her to stay but at the briefing she felt the urge to join them so she left and changed for the negotiations before joining them. The planet was cool with clouds blotting out the sun.

As they walked on she thought she heard someone in the trees but when she looked over no one was there. The second time she thought she heard she wandered over to the trees but found no evidence that anyone had been there in some time. As she reentered the group one of the friendlier ambassadors walked up next to her, "What were you doing over there?"

"I thought I had heard something it was nothing."

"Looked secluded we could slip in there for a bit for some privacy," he smiled hoping to charm her.

"No," she said her tone indicating that she did not wish to talk. The ambassador fell in with his other friends who began talking about what she presumed was her actions towards him. Most on Atlantis knew that she was John's, but a few either didn't know or didn't care. It had created some problems for her occasional but she was normally able to deflect their advances easily but today she was not in the mood. As the team walked on she spotted some flowers on the side of the road they reminded her of some she had seen on Atlantis roses Rodney had called them. Confused as to why an Earth flower was here a world they had never contacted before she bent down to collect it. When her hand touched the flower she felt the wind blow softly against her hand she smiled. He wasn't asking for anything just a reminder to her that he was there with her if she wanted anything. He had put the flower there.

The team continued down the road towards the village and most of the complaints died away except for one who she knew would never stop complaining he was just too much like Rodney. She frowned at the thought of Rodney, they had all tried to keep in touch but it was difficult when they were all busy. For her rarely a day went by when she wasn't supposed to be negotiating with some new world to try and join the Republic. Ronon was building and overseeing the entire Pegasus army a task he both loved and hated. Rodney was the busiest of all Head of Science for the Republic and he was involved in almost every scientific project from both Galaxies. And John well no one knew how busy he was as far as she knew he didn't have a single obligation but as far as anyone else was concerned he was not available. The others smiled at her when she returned to their procession with the small flower.

After several hours of walking they came to a point where the road stopped for what looked to be at least a quarter of a mile before it started again. As the group made their way across the grass she saw a shadow amongst the trees. She moved out of the group to investigate. As she stepped out of the group she heard a staccato of gunfire. She reached for her sidearm before realizing that she hadn't carried it on the mission because some natives were afraid of their weapons and she did not wish to risk freighting these natives unnecessarily. Teyla dove into the ground trying to avoid the weapons fire. A woman screamed a moment later and she recognized it as the scream of a rookie negotiator; when she turned around she saw the dead bodies and the woman fell a second later silencing her screams.

Men slowly walked out of the forest armed with P90's but not wearing any uniforms they encircled her their weapons aimed while some dragged the bodies away into the forest. "Who are you?"She asked not with fear, but anger. She wanted revenge for the deaths of her colleagues.

None of them responded and the ones who dragged the bodies away returned to their positions in the tight circle. "Who are you?" she repeated but still none of them answered but she saw another figure exiting the shadows of the forest. As he approached the group the two men in front of him parted allowing him entrance, "They serve me Teyla," his voice had an immediate negative effect on her as her eyes blazed with hate and anger.

"Why did you kill these people?"

"I did not need them," he responded as Teyla attempted to attack one of his guards but was forced back by his gun. When she fell back into the circle he smiled at her, "You never did know when to accept defeat," he spat; their hatred of each other etched in their faces for all to see. A cruel smile formed on his lips, "I want to hear you beg for it like you begged for me to screw you," he said taking out his pistol and aiming it at her head.

"You will pay for this," she said rising to her feet. She saw what they're parting had done to him, he was not the man she knew anymore he had twisted his memory and reality to suit his needs.

"You first," the round echoed silently as it impacted against a white shield that had appeared in front of Teyla's now smiling face.

"John," she whispered quietly as she felt the wind whip around her blowing her hair around she felt his hand on her cheek as he resolved himself around her.

"Hello Teyla," he stared into her eyes before claiming her lips in a quick kiss. When they broke he turned around growling.

"I TOLD YOU TO RUN AND HIDE," he screamed causing everyone to jump back a couple of feet. Kanaan only smiled in response as John advanced upon him. "Perhaps I should emphasize my point," he closed his eyes for a moment and when he opened them the look he gave Kanaan was that of a predator stalking its prey without breaking eye contact he casually gestured towards the guards. When Kanaan looked at his men they had all fallen to the ground dead, "You will not be so lucky."

His face drained, fear filled him, he swallowed still in disbelief at how quickly his position had changed, "YOU SEE WHO HE IS TEYLA IF YOU GO AGAINST HIM HE'LL DESTROY YOU," he screamed at Teyla as he slowly backed away from John towards the forest. John stood there between Teyla, who was checking the life signs of the men who had recently fallen, and the slowly retreating Kanaan.

"No you'll pay for trying to kill Teyla," hearing his words Teyla stood up quickly she didn't want Kanaan to be tortured or killed by John; she knew that he wouldn't be allowed to live after what he had just done but Kanaan was her responsibility not John's.

She faced him sadness in her eyes, "John do not. We will deal with him," she said aiming the weapon she had stolen from the corpse at him.

He turned to face her she saw in his eyes her betrayal, "You would kill me to save him?"

"No, he is not yours to kill. I must be the one to end it, not you." She was barely able to keep the gun straight. His eyes flickered up to hers and for the first time she saw sadness in them, "John do not make me do this," she begged. The sadness in his eyes evaporated replaced with something she didn't understand his hand reached down for his weapon. She couldn't allow him to kill Kanaan and as his hand reached his own weapon one shot rang out. He felt its impact and his eyes found and held hers attempting to convey everything he didn't have the time to tell her. The blood began seeping through his clothes as he hit the ground. She looked at Kanaan who had a self-satisfied smile on his face back to John who was lying on the ground in pain but refusing to show it. She found his gaze once more and saw not a trace of any anger, betrayal, or hate but his love for her. She walked towards his body slowly leveling her gun she heard the four rounds ring out and knew that he was dead. She dropped her gun and fell to the grass beside John as tears made their way down her cheeks. As she opened her eyes she felt a warm presence beside her and when she opened her eyes there was a bright light in front of her, "John?"

"He is gravely injured you should not have threatened him," a familiar voice responded.

"Ganos?"

"Yes Teyla we are here helping him," she said moving to show Teyla the others.

"Is that not against your highest rules?"

"We made an exception in this case he is after all ascended."

"Thank you," she said getting up and knelling next to John. She took his face in her hand and whispered something in his ear before getting up and leaving the Ancients to their work. She walked over towards where Ganos had remained waiting for her, "Today was to be my last mission I had planned to join John before returning to Atlantis today."

"Then why did you threaten him?"

"I could not allow him to harm Kanaan."

"But did you not shoot Kanaan only moments after he shot John?"

"I did Kanaan was my responsibility not John's."

"Well Teyla I hope you do get to join him you both deserve it."

"Really though how close were you two if you were involved it would not change my decision."

"We were just friends in fact I was the first person he told when he saw you. That was a huge risk on his part because we were negotiating to get him to stop interfering at the time but he knew I wouldn't reveal that he would be taking human form in the future."

"Why was I such a big secret?"

"Because Teyla if they knew about you they would have attempted to stop John from retaking human form and meeting you. With the two of you interfering the council would be continually attempting to stop you two."

"Will he be okay?"

"I do not know I must attend to himself goodbye and good luck Teyla."

She waited in the field for the rest of the day hoping that John would appear again, "Teyla?" She turned around trying to identify the source of the voice. It wasn't anyone she was familiar with.

"Yes, who are you?"

"I am Plato, Ganos told me to find you and tell you that John should recover."

"How long?"

"A few hours probably, you should stay in the village."

"Thank you."

***

Teyla awoke calmly staring at John's natural form, "I'm sorry I wouldn't have ever-"

"I know."

"You don't look well."

"I'm not."

"Can you still…"

"What?" He was confused.

"Does your offer still stand?"

"To join me?"

"Yes."

John stared her in the eyes and saw her resolve, "take my hand."

She complied without hesitation finally ready to accept whatever John was offering her.

He smiled as they embarked upon their journey together, for the first time he brought someone else into his realm.

A/N- I apologize for the horrible updating, I failed my duty as an author. I'm sorry.

Thank you everyone who reviewed despite my horrible updating.

End of Secrets

My other fics will eventually be finished, sorry about them all. Again you guys have my apologies not that that really means much.


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